diff --git a/cwltool/builder.py b/cwltool/builder.py
index 844c585c6..a417eeedb 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -6,7 +6,7 @@
 from typing import Any, Union, AnyStr, Callable
 from .errors import WorkflowException
 from .stdfsaccess import StdFsAccess
-from .pathmapper import PathMapper
+from .pathmapper import PathMapper, adjustFileObjs, adjustDirObjs
 
 CONTENT_LIMIT = 64 * 1024
 
@@ -17,18 +17,6 @@ def substitute(value, replace):  # type: (str, str) -> str
     else:
         return value + replace
 
-def adjustFileObjs(rec, op):  # type: (Any, Callable[[Any], Any]) -> None
-    """Apply an update function to each File object in the object `rec`."""
-
-    if isinstance(rec, dict):
-        if rec.get("class") == "File":
-            op(rec)
-        for d in rec:
-            adjustFileObjs(rec[d], op)
-    if isinstance(rec, list):
-        for d in rec:
-            adjustFileObjs(d, op)
-
 class Builder(object):
 
     def __init__(self):  # type: () -> None
@@ -114,7 +102,7 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
             if schema["type"] == "File":
                 self.files.append(datum)
                 if binding and binding.get("loadContents"):
-                    with self.fs_access.open(datum["path"], "rb") as f:
+                    with self.fs_access.open(datum["location"], "rb") as f:
                         datum["contents"] = f.read(CONTENT_LIMIT)
 
                 if "secondaryFiles" in schema:
@@ -124,11 +112,11 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
                         if isinstance(sf, dict) or "$(" in sf or "${" in sf:
                             secondary_eval = self.do_eval(sf, context=datum)
                             if isinstance(secondary_eval, basestring):
-                                sfpath = {"path": secondary_eval, "class": "File"}
+                                sfpath = {"location": secondary_eval, "class": "File"}
                             else:
                                 sfpath = secondary_eval
                         else:
-                            sfpath = {"path": substitute(datum["path"], sf), "class": "File"}
+                            sfpath = {"location": substitute(datum["location"], sf), "class": "File"}
                         if isinstance(sfpath, list):
                             datum["secondaryFiles"].extend(sfpath)
                         else:
@@ -140,6 +128,10 @@ def _capture_files(f):
 
                 adjustFileObjs(datum.get("secondaryFiles", []), _capture_files)
 
+            if schema["type"] == "Directory":
+                self.files.append(datum)
+
+
         # Position to front of the sort key
         if binding:
             for bi in bindings:
diff --git a/cwltool/cwltest.py b/cwltool/cwltest.py
index 8b37ce390..a7b7f95ff 100755
--- a/cwltool/cwltest.py
+++ b/cwltool/cwltest.py
@@ -37,10 +37,30 @@ def compare(a, b):  # type: (Any, Any) -> bool
                 # ignore empty collections
                 b = {k: v for k, v in b.iteritems()
                      if not isinstance(v, (list, dict)) or len(v) > 0}
+            elif a.get("class") == "Directory":
+                if len(a["listing"]) != len(b["listing"]):
+                    return False
+                for i in a["listing"]:
+                    found = False
+                    for j in b["listing"]:
+                        try:
+                            if compare(i, j):
+                                found = True
+                                break
+                        except:
+                            pass
+                    if not found:
+                        raise CompareFail(u"%s not in %s" % (json.dumps(i, indent=4, sort_keys=True), json.dumps(b, indent=4, sort_keys=True)))
+
+            a = {k: v for k, v in a.iteritems()
+                 if k not in ("path", "location", "listing")}
+            b = {k: v for k, v in b.iteritems()
+                 if k not in ("path", "location", "listing")}
+
             if len(a) != len(b):
                 raise CompareFail(u"expected %s\ngot %s" % (json.dumps(a, indent=4, sort_keys=True), json.dumps(b, indent=4, sort_keys=True)))
             for c in a:
-                if a.get("class") != "File" or c != "path":
+                if a.get("class") != "File" or c not in ("path", "location", "listing"):
                     if c not in b:
                         raise CompareFail(u"%s not in %s" % (c, b))
                     if not compare(a[c], b[c]):
diff --git a/cwltool/draft2tool.py b/cwltool/draft2tool.py
index 39fbaed48..d74199b31 100644
--- a/cwltool/draft2tool.py
+++ b/cwltool/draft2tool.py
@@ -1,29 +1,34 @@
-import avro.schema
+import shutil
+from functools import partial
 import json
 import copy
-from .flatten import flatten
-from functools import partial
 import os
-from .pathmapper import PathMapper, DockerPathMapper
-from .job import CommandLineJob
 import glob
 import logging
 import hashlib
 import random
-from .process import Process, shortname, uniquename, adjustFileObjs
-from .errors import WorkflowException
-import schema_salad.validate as validate
-from .utils import aslist
-from . import expression
 import re
 import urlparse
 import tempfile
-from .builder import CONTENT_LIMIT, substitute, Builder
-import shellescape
 import errno
+
+import avro.schema
+import yaml
+import schema_salad.validate as validate
+import shellescape
 from typing import Callable, Any, Union, Generator, cast
-import hashlib
-import shutil
+
+from .process import Process, shortname, uniquename, getListing
+from .errors import WorkflowException
+from .utils import aslist
+from . import expression
+from .builder import CONTENT_LIMIT, substitute, Builder, adjustFileObjs, adjustDirObjs
+from .pathmapper import PathMapper
+from .job import CommandLineJob
+
+ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._-]+$")
+
+from .flatten import flatten
 
 _logger = logging.getLogger("cwltool")
 
@@ -67,10 +72,9 @@ def job(self, joborder, output_callback, **kwargs):
         yield j
 
 
-def remove_hostfs(f):  # type: (Dict[str, Any]) -> None
-    if "hostfs" in f:
-        del f["hostfs"]
-
+def remove_path(f):  # type: (Dict[str, Any]) -> None
+    if "path" in f:
+        del f["path"]
 
 def revmap_file(builder, outdir, f):
     # type: (Builder,str,Dict[str,Any]) -> Union[Dict[str,Any],None]
@@ -80,17 +84,15 @@ def revmap_file(builder, outdir, f):
     to the external directory.
     """
 
-    if f.get("hostfs"):
-        return None
+    if "location" in f:
+        return f
 
     revmap_f = builder.pathmapper.reversemap(f["path"])
     if revmap_f:
-        f["path"] = revmap_f[1]
-        f["hostfs"] = True
+        f["location"] = revmap_f[1]
         return f
     elif f["path"].startswith(builder.outdir):
-        f["path"] = os.path.join(outdir, f["path"][len(builder.outdir)+1:])
-        f["hostfs"] = True
+        f["location"] = os.path.join(outdir, f["path"][len(builder.outdir)+1:])
         return f
     else:
         raise WorkflowException(u"Output file path %s must be within designated output directory (%s) or an input file pass through." % (f["path"], builder.outdir))
@@ -118,14 +120,11 @@ def __init__(self, toolpath_object, **kwargs):
     def makeJobRunner(self):  # type: () -> CommandLineJob
         return CommandLineJob()
 
-    def makePathMapper(self, reffiles, **kwargs):
-        # type: (Set[unicode], **Any) -> PathMapper
+    def makePathMapper(self, reffiles, stagedir, **kwargs):
+        # type: (Set[Any], unicode, **Any) -> PathMapper
         dockerReq, _ = self.get_requirement("DockerRequirement")
         try:
-            if dockerReq and kwargs.get("use_container"):
-                return DockerPathMapper(reffiles, kwargs["basedir"])
-            else:
-                return PathMapper(reffiles, kwargs["basedir"])
+            return PathMapper(reffiles, kwargs["basedir"], stagedir)
         except OSError as e:
             if e.errno == errno.ENOENT:
                 raise WorkflowException(u"Missing input file %s" % e)
@@ -139,9 +138,11 @@ def job(self, joborder, output_callback, **kwargs):
             cacheargs = kwargs.copy()
             cacheargs["outdir"] = "/out"
             cacheargs["tmpdir"] = "/tmp"
+            cacheargs["stagedir"] = "/stage"
             cachebuilder = self._init_job(joborder, **cacheargs)
-            cachebuilder.pathmapper = PathMapper(set((f["path"] for f in cachebuilder.files)),
-                                                 kwargs["basedir"])
+            cachebuilder.pathmapper = PathMapper(cachebuilder.files,
+                                                 kwargs["basedir"],
+                                                 cachebuilder.stagedir)
 
             cmdline = flatten(map(cachebuilder.generate_arg, cachebuilder.bindings))
             (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
@@ -199,7 +200,7 @@ def rm_pending_output_callback(output_callback, jobcachepending,
 
         builder = self._init_job(joborder, **kwargs)
 
-        reffiles = set((f[u"path"] for f in builder.files))
+        reffiles = copy.deepcopy(builder.files)
 
         j = self.makeJobRunner()
         j.builder = builder
@@ -223,10 +224,6 @@ def rm_pending_output_callback(output_callback, jobcachepending,
 
         builder.pathmapper = None
 
-        if self.tool.get("stdin"):
-            j.stdin = builder.do_eval(self.tool["stdin"])
-            reffiles.add(j.stdin)
-
         if self.tool.get("stderr"):
             j.stderr = builder.do_eval(self.tool["stderr"])
             if os.path.isabs(j.stderr) or ".." in j.stderr:
@@ -234,42 +231,57 @@ def rm_pending_output_callback(output_callback, jobcachepending,
 
         if self.tool.get("stdout"):
             j.stdout = builder.do_eval(self.tool["stdout"])
-            if os.path.isabs(j.stdout) or ".." in j.stdout:
+            if os.path.isabs(j.stdout) or ".." in j.stdout or not j.stdout:
                 raise validate.ValidationException("stdout must be a relative path")
 
-        builder.pathmapper = self.makePathMapper(reffiles, **kwargs)
+        builder.pathmapper = self.makePathMapper(reffiles, builder.stagedir, **kwargs)
         builder.requirements = j.requirements
 
         # map files to assigned path inside a container. We need to also explicitly
         # walk over input as implicit reassignment doesn't reach everything in builder.bindings
         def _check_adjust(f):  # type: (Dict[str,Any]) -> Dict[str,Any]
-            if not f.get("containerfs"):
-                f["path"] = builder.pathmapper.mapper(f["path"])[1]
-                f["containerfs"] = True
+            f["path"] = builder.pathmapper.mapper(f["location"])[1]
+            f["dirname"], f["basename"] = os.path.split(f["path"])
+            if f["class"] == "File":
+                f["nameroot"], f["nameext"] = os.path.splitext(f["basename"])
+            if not ACCEPTLIST_RE.match(f["basename"]):
+                raise WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"]))
             return f
 
         _logger.debug(u"[job %s] path mappings is %s", j.name, json.dumps({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}, indent=4))
 
         adjustFileObjs(builder.files, _check_adjust)
         adjustFileObjs(builder.bindings, _check_adjust)
+        adjustDirObjs(builder.files, _check_adjust)
+        adjustDirObjs(builder.bindings, _check_adjust)
+
+        if self.tool.get("stdin"):
+            j.stdin = builder.do_eval(self.tool["stdin"])
+            reffiles.append({"class": "File", "path": j.stdin})
 
         _logger.debug(u"[job %s] command line bindings is %s", j.name, json.dumps(builder.bindings, indent=4))
 
-        dockerReq = self.get_requirement("DockerRequirement")[0]
+        dockerReq, _ = self.get_requirement("DockerRequirement")
         if dockerReq and kwargs.get("use_container"):
             out_prefix = kwargs.get("tmp_outdir_prefix")
             j.outdir = kwargs.get("outdir") or tempfile.mkdtemp(prefix=out_prefix)
             tmpdir_prefix = kwargs.get('tmpdir_prefix')
             j.tmpdir = kwargs.get("tmpdir") or tempfile.mkdtemp(prefix=tmpdir_prefix)
+            j.stagedir = None
         else:
             j.outdir = builder.outdir
             j.tmpdir = builder.tmpdir
+            j.stagedir = builder.stagedir
 
-        createFiles = self.get_requirement("CreateFileRequirement")[0]
-        j.generatefiles = {}
-        if createFiles:
-            for t in createFiles["fileDef"]:
-                j.generatefiles[builder.do_eval(t["filename"])] = copy.deepcopy(builder.do_eval(t["fileContent"]))
+        initialWorkdir = self.get_requirement("InitialWorkDirRequirement")[0]
+        j.generatefiles = {"class": "Directory", "listing": []}
+        if initialWorkdir:
+            if isinstance(initialWorkdir["listing"], (str, unicode)):
+                j.generatefiles["listing"] = builder.do_eval(initialWorkdir["listing"])
+            else:
+                for t in initialWorkdir["listing"]:
+                    j.generatefiles["listing"].append({"entryname": builder.do_eval(t["entryname"]),
+                                                       "entry": copy.deepcopy(builder.do_eval(t["entry"]))})
 
         j.environment = {}
         evr = self.get_requirement("EnvVarRequirement")[0]
@@ -305,12 +317,11 @@ def collect_output_ports(self, ports, builder, outdir):
                 with builder.fs_access.open(custom_output, "r") as f:
                     ret = json.load(f)
                 _logger.debug(u"Raw output from %s: %s", custom_output, json.dumps(ret, indent=4))
-                adjustFileObjs(ret, remove_hostfs)
                 adjustFileObjs(ret,
                         cast(Callable[[Any], Any],  # known bug in mypy
                             # https://github.com/python/mypy/issues/797
                             partial(revmap_file, builder, outdir)))
-                adjustFileObjs(ret, remove_hostfs)
+                adjustFileObjs(ret, remove_path)
                 validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
                 return ret
 
@@ -319,9 +330,11 @@ def collect_output_ports(self, ports, builder, outdir):
                 try:
                     ret[fragment] = self.collect_output(port, builder, outdir)
                 except Exception as e:
+                    _logger.debug(u"Error collecting output for parameter '%s'" % shortname(port["id"]), exc_info=e)
                     raise WorkflowException(u"Error collecting output for parameter '%s': %s" % (shortname(port["id"]), e))
             if ret:
-                adjustFileObjs(ret, remove_hostfs)
+                adjustFileObjs(ret, remove_path)
+                adjustDirObjs(ret, remove_path)
             validate.validate_ex(self.names.get_name("outputs_record_schema", ""), ret)
             return ret if ret is not None else {}
         except validate.ValidationException as e:
@@ -345,60 +358,50 @@ def collect_output(self, schema, builder, outdir):
                 for gb in globpatterns:
                     if gb.startswith(outdir):
                         gb = gb[len(outdir)+1:]
+                    elif gb == ".":
+                        gb = outdir
                     elif gb.startswith("/"):
                         raise WorkflowException("glob patterns must not start with '/'")
                     try:
-                        r.extend([{"path": g, "class": "File", "hostfs": True}
+                        r.extend([{"location": g,
+                                   "class": "File" if builder.fs_access.isfile(g) else "Directory"}
                                   for g in builder.fs_access.glob(os.path.join(outdir, gb))])
                     except (OSError, IOError) as e:
                         _logger.warn(str(e))
 
                 for files in r:
-                    checksum = hashlib.sha1()
-                    with builder.fs_access.open(files["path"], "rb") as f:
-                        contents = f.read(CONTENT_LIMIT)
-                        if binding.get("loadContents"):
-                            files["contents"] = contents
-                        filesize = 0
-                        while contents != "":
-                            checksum.update(contents)
-                            filesize += len(contents)
-                            contents = f.read(1024*1024)
-                    files["checksum"] = "sha1$%s" % checksum.hexdigest()
-                    files["size"] = filesize
-                    if "format" in schema:
-                        files["format"] = builder.do_eval(schema["format"], context=files)
+                    if files["class"] == "Directory" and "listing" not in files:
+                        getListing(builder.fs_access, files)
+                    else:
+                        checksum = hashlib.sha1()
+                        with builder.fs_access.open(files["location"], "rb") as f:
+                            contents = f.read(CONTENT_LIMIT)
+                            if binding.get("loadContents"):
+                                files["contents"] = contents
+                            filesize = 0
+                            while contents != "":
+                                checksum.update(contents)
+                                filesize += len(contents)
+                                contents = f.read(1024*1024)
+                        files["checksum"] = "sha1$%s" % checksum.hexdigest()
+                        files["size"] = filesize
+                        if "format" in schema:
+                            files["format"] = builder.do_eval(schema["format"], context=files)
 
             optional = False
-            singlefile = False
+            single = False
             if isinstance(schema["type"], list):
                 if "null" in schema["type"]:
                     optional = True
-                if "File" in schema["type"]:
-                    singlefile = True
-            elif schema["type"] == "File":
-                singlefile = True
+                if "File" in schema["type"] or "Directory" in schema["type"]:
+                    single = True
+            elif schema["type"] == "File" or schema["type"] == "Directory":
+                single = True
 
             if "outputEval" in binding:
-                eout = builder.do_eval(binding["outputEval"], context=r)
-                if singlefile:
-                    # Handle single file outputs not wrapped in a list
-                    if eout is not None and not isinstance(eout, (list, tuple)):
-                        r = [eout]
-                    elif optional and eout is None:
-                        pass
-                    elif (eout is None or len(eout) != 1 or
-                            not isinstance(eout[0], dict)
-                            or "path" not in eout[0]):
-                        raise WorkflowException(
-                            u"Expression must return a file object for %s."
-                            % schema["id"])
-                    else:
-                        r = [eout]
-                else:
-                    r = eout
+                r = builder.do_eval(binding["outputEval"], context=r)
 
-            if singlefile:
+            if single:
                 if not r and not optional:
                     raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
                 elif not r and optional:
@@ -420,14 +423,14 @@ def collect_output(self, schema, builder, outdir):
                         primary["secondaryFiles"] = []
                         for sf in aslist(schema["secondaryFiles"]):
                             if isinstance(sf, dict) or "$(" in sf or "${" in sf:
-                                sfpath = builder.do_eval(sf, context=r)
+                                sfpath = builder.do_eval(sf, context=primary)
                                 if isinstance(sfpath, basestring):
-                                    sfpath = revmap({"path": sfpath, "class": "File"})
+                                    sfpath = revmap({"location": sfpath, "class": "File"})
                             else:
-                                sfpath = {"path": substitute(primary["path"], sf), "class": "File", "hostfs": True}
+                                sfpath = {"location": substitute(primary["location"], sf), "class": "File"}
 
                             for sfitem in aslist(sfpath):
-                                if builder.fs_access.exists(sfitem["path"]):
+                                if builder.fs_access.exists(sfitem["location"]):
                                     primary["secondaryFiles"].append(sfitem)
 
             if not r and optional:
diff --git a/cwltool/job.py b/cwltool/job.py
index 01b3d7c14..539c2f37e 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -8,7 +8,7 @@
 import sys
 import requests
 from . import docker
-from .process import get_feature, empty_subtree
+from .process import get_feature, empty_subtree, stageFiles
 from .errors import WorkflowException
 import shutil
 import stat
@@ -61,7 +61,7 @@ def __init__(self):  # type: () -> None
         self.generatefiles = None  # type: Dict[str,Union[Dict[str,str],str]]
 
     def run(self, dry_run=False, pull_image=True, rm_container=True,
-            rm_tmpdir=True, move_outputs=True, **kwargs):
+            rm_tmpdir=True, move_outputs="move", **kwargs):
         # type: (bool, bool, bool, bool, bool, **Any) -> Union[Tuple[str,Dict[None,None]],None]
         if not os.path.exists(self.outdir):
             os.makedirs(self.outdir)
@@ -79,8 +79,9 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
 
         for f in self.pathmapper.files():
-            if not os.path.isfile(self.pathmapper.mapper(f)[0]):
-                raise WorkflowException(u"Required input file %s not found or is not a regular file." % self.pathmapper.mapper(f)[0])
+            p = self.pathmapper.mapper(f)
+            if p.type == "File" and not os.path.isfile(p[0]):
+                raise WorkflowException(u"Input file %s (at %s) not found or is not a regular file." % (f, self.pathmapper.mapper(f)[0]))
 
         img_id = None
         if docker_req and kwargs.get("use_container") is not False:
@@ -94,7 +95,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
             runtime = ["docker", "run", "-i"]
             for src in self.pathmapper.files():
                 vol = self.pathmapper.mapper(src)
-                runtime.append(u"--volume=%s:%s:ro" % vol)
+                if vol.type == "File":
+                    runtime.append(u"--volume=%s:%s:ro" % (vol.resolved, vol.target))
             runtime.append(u"--volume=%s:%s:rw" % (os.path.abspath(self.outdir), "/var/spool/cwl"))
             runtime.append(u"--volume=%s:%s:rw" % (os.path.abspath(self.tmpdir), "/tmp"))
             runtime.append(u"--workdir=%s" % ("/var/spool/cwl"))
@@ -136,6 +138,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
                     if key in vars_to_preserve and key not in env:
                         env[key] = value
 
+            stageFiles(self.pathmapper, os.symlink)
+
         stdin = None  # type: Union[IO[Any],int]
         stderr = None  # type: IO[Any]
         stdout = None  # type: IO[Any]
@@ -151,7 +155,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
                      self.name,
                      self.outdir,
                      " \\\n    ".join([shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg) for arg in (runtime + self.command_line)]),
-                     u' < %s' % (self.stdin) if self.stdin else '',
+                     u' < %s' % self.stdin if self.stdin else '',
                      u' > %s' % os.path.join(self.outdir, self.stdout) if self.stdout else '',
                      u' 2> %s' % os.path.join(self.outdir, self.stderr) if self.stderr else '')
 
@@ -161,22 +165,22 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
         outputs = {}  # type: Dict[str,str]
 
         try:
-            for t in self.generatefiles:
-                entry = self.generatefiles[t]
-                if isinstance(entry, dict):
-                    src = entry["path"]
-                    dst = os.path.join(self.outdir, t)
-                    if os.path.dirname(self.pathmapper.reversemap(src)[1]) != self.outdir:
-                        _logger.debug(u"symlinking %s to %s", dst, src)
-                        os.symlink(src, dst)
-                elif isinstance(entry, (str, unicode)):
-                    with open(os.path.join(self.outdir, t), "w") as fout:
-                        fout.write(entry.encode("utf-8"))
-                else:
-                    raise Exception("Unhandled type %s", type(entry))
+            if self.generatefiles["listing"]:
+                generatemapper = PathMapper([self.generatefiles], self.outdir,
+                                            self.outdir, separateDirs=False)
+                _logger.debug(u"[job %s] initial work dir %s", self.name,
+                              json.dumps({p: generatemapper.mapper(p) for p in generatemapper.files()}, indent=4))
+                def linkoutdir(src, tgt):
+                    # Need to make the link to the staged file (may be inside
+                    # the container)
+                    for _, item in self.pathmapper.items():
+                        if src == item.resolved:
+                            os.symlink(item.target, tgt)
+                            break
+                stageFiles(generatemapper, linkoutdir)
 
             if self.stdin:
-                stdin = open(self.pathmapper.mapper(self.stdin)[0], "rb")
+                stdin = open(self.pathmapper.reversemap(self.stdin)[1], "rb")
             else:
                 stdin = subprocess.PIPE
 
@@ -198,7 +202,7 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
             else:
                 stdout = sys.stderr
 
-            sp = subprocess.Popen([str(x) for x in runtime + self.command_line],
+            sp = subprocess.Popen([unicode(x).encode('utf-8') for x in runtime + self.command_line],
                                   shell=False,
                                   close_fds=True,
                                   stdin=stdin,
@@ -232,13 +236,14 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
             else:
                 processStatus = "permanentFail"
 
-            for t in self.generatefiles:
-                if isinstance(self.generatefiles[t], dict):
-                    src = cast(dict, self.generatefiles[t])["path"]
-                    dst = os.path.join(self.outdir, t)
-                    if os.path.dirname(self.pathmapper.reversemap(src)[1]) != self.outdir:
-                        os.remove(dst)
-                        os.symlink(self.pathmapper.reversemap(src)[1], dst)
+            if self.generatefiles["listing"]:
+                def linkoutdir(src, tgt):
+                    # Need to make the link to the staged file (may be inside
+                    # the container)
+                    if os.path.exists(tgt) and os.path.islink(tgt):
+                        os.remove(tgt)
+                        os.symlink(src, tgt)
+                stageFiles(generatemapper, linkoutdir)
 
             outputs = self.collect_outputs(self.outdir)
 
@@ -266,10 +271,14 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
 
         self.output_callback(outputs, processStatus)
 
+        if self.stagedir and os.path.exists(self.stagedir):
+            _logger.debug(u"[job %s] Removing input staging directory %s", self.name, self.stagedir)
+            shutil.rmtree(self.stagedir, True)
+
         if rm_tmpdir:
             _logger.debug(u"[job %s] Removing temporary directory %s", self.name, self.tmpdir)
             shutil.rmtree(self.tmpdir, True)
 
-        if move_outputs and empty_subtree(self.outdir):
+        if move_outputs == "move" and empty_subtree(self.outdir):
             _logger.debug(u"[job %s] Removing empty output directory %s", self.name, self.outdir)
             shutil.rmtree(self.outdir, True)
diff --git a/cwltool/main.py b/cwltool/main.py
index b86995115..1bd3f14a7 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -1,31 +1,37 @@
 #!/usr/bin/env python
 
-from . import draft2tool
 import argparse
-from schema_salad.ref_resolver import Loader
 import string
 import json
 import os
 import sys
 import logging
 import copy
-from . import workflow
-from .errors import WorkflowException, UnsupportedRequirement
-from . import process
-from .cwlrdf import printrdf, printdot
-from .process import shortname, Process
-from .load_tool import fetch_document, validate_document, make_tool
-import schema_salad.validate as validate
 import tempfile
-import schema_salad.jsonld_context
-import schema_salad.makedoc
 import ruamel.yaml as yaml
 import urlparse
+import hashlib
 import pkg_resources  # part of setuptools
+import random
+import functools
+
 import rdflib
-import hashlib
 from typing import Union, Any, cast, Callable, Dict, Tuple, IO
 
+from schema_salad.ref_resolver import Loader
+import schema_salad.validate as validate
+import schema_salad.jsonld_context
+import schema_salad.makedoc
+
+from . import workflow
+from .errors import WorkflowException, UnsupportedRequirement
+from .cwlrdf import printrdf, printdot
+from .process import shortname, Process, getListing, relocateOutputs, cleanIntermediate, scandeps
+from .load_tool import fetch_document, validate_document, make_tool
+from . import draft2tool
+from .builder import adjustFileObjs, adjustDirObjs
+from .stdfsaccess import StdFsAccess
+
 _logger = logging.getLogger("cwltool")
 
 defaultStreamHandler = logging.StreamHandler()
@@ -81,14 +87,18 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         dest="rm_tmpdir")
 
     exgroup = parser.add_mutually_exclusive_group()
-    exgroup.add_argument("--move-outputs", action="store_true", default=True,
+    exgroup.add_argument("--move-outputs", action="store_const", const="move", default="move",
                         help="Move output files to the workflow output directory and delete intermediate output directories (default).",
                         dest="move_outputs")
 
-    exgroup.add_argument("--leave-outputs", action="store_false", default=True,
+    exgroup.add_argument("--leave-outputs", action="store_const", const="leave", default="move",
                         help="Leave output files in intermediate output directories.",
                         dest="move_outputs")
 
+    exgroup.add_argument("--copy-outputs", action="store_const", const="copy", default="move",
+                         help="Copy output files to the workflow output directory, don't delete intermediate output directories.",
+                         dest="move_outputs")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-pull", default=True, action="store_true",
                         help="Try to pull Docker images", dest="enable_pull")
@@ -167,12 +177,10 @@ def output_callback(out, processStatus):
     if "basedir" not in kwargs:
         raise WorkflowException("Must provide 'basedir' in kwargs")
 
-    if kwargs.get("outdir"):
-        pass
-    elif kwargs.get("dry_run"):
-        kwargs["outdir"] = "/tmp"
-    else:
-        kwargs["outdir"] = tempfile.mkdtemp()
+    output_dirs = set()
+    finaloutdir = kwargs.get("outdir")
+    kwargs["outdir"] = tempfile.mkdtemp()
+    output_dirs.add(kwargs["outdir"])
 
     jobReqs = None
     if "cwl:requirements" in job_order_object:
@@ -188,35 +196,32 @@ def output_callback(out, processStatus):
                     output_callback,
                     **kwargs)
 
-    if kwargs.get("conformance_test"):
-        job = jobiter.next()
-        a = {"args": job.command_line}
-        if job.stdin:
-            a["stdin"] = job.pathmapper.mapper(job.stdin)[1]
-        if job.stderr:
-            a["stderr"] = job.stderr
-        if job.stdout:
-            a["stdout"] = job.stdout
-        if job.generatefiles:
-            a["createfiles"] = job.generatefiles
-        return a
-    else:
-        try:
-            for r in jobiter:
-                if r:
-                    r.run(**kwargs)
-                else:
-                    raise WorkflowException("Workflow cannot make any more progress.")
-        except WorkflowException:
-            raise
-        except Exception as e:
-            _logger.exception("Got workflow error")
-            raise WorkflowException(unicode(e))
+    try:
+        for r in jobiter:
+            if r.outdir:
+                output_dirs.add(r.outdir)
+
+            if r:
+                r.run(**kwargs)
+            else:
+                raise WorkflowException("Workflow cannot make any more progress.")
+    except WorkflowException:
+        raise
+    except Exception as e:
+        _logger.exception("Got workflow error")
+        raise WorkflowException(unicode(e))
 
-        if final_status[0] != "success":
-            raise WorkflowException(u"Process status is %s" % (final_status))
+    if final_status[0] != "success":
+        raise WorkflowException(u"Process status is %s" % (final_status))
 
-        return final_output[0]
+    if final_output[0] and finaloutdir:
+        final_output[0] = relocateOutputs(final_output[0], finaloutdir,
+                                          output_dirs, kwargs.get("move_outputs"))
+
+    if kwargs.get("rm_tmpdir"):
+        cleanIntermediate(output_dirs)
+
+    return final_output[0]
 
 
 class FileAction(argparse.Action):
@@ -229,7 +234,20 @@ def __init__(self, option_strings, dest, nargs=None, **kwargs):
 
     def __call__(self, parser, namespace, values, option_string=None):
         # type: (argparse.ArgumentParser, argparse.Namespace, str, Any) -> None
-        setattr(namespace, self.dest, {"class": "File", "path": values})
+        setattr(namespace, self.dest, {"class": "File", "location": "file://%s" % os.path.abspath(values)})
+
+
+class DirectoryAction(argparse.Action):
+
+    def __init__(self, option_strings, dest, nargs=None, **kwargs):
+        # type: (List[str], str, Any, **Any) -> None
+        if nargs is not None:
+            raise ValueError("nargs not allowed")
+        super(DirectoryAction, self).__init__(option_strings, dest, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        # type: (argparse.ArgumentParser, argparse.Namespace, str, Any) -> None
+        setattr(namespace, self.dest, {"class": "Directory", "location": "file://%s" % os.path.abspath(values)})
 
 
 class FileAppendAction(argparse.Action):
@@ -246,7 +264,7 @@ def __call__(self, parser, namespace, values, option_string=None):
         if not g:
             g = []
             setattr(namespace, self.dest, g)
-        g.append({"class": "File", "path": values})
+        g.append({"class": "File", "location": "file://%s" % os.path.abspath(values)})
 
 
 def generate_parser(toolparser, tool, namemap):
@@ -282,6 +300,8 @@ def generate_parser(toolparser, tool, namemap):
 
         if inptype == "File":
             action = cast(argparse.Action, FileAction)
+        elif inptype == "Directory":
+            action = cast(argparse.Action, DirectoryAction)
         elif isinstance(inptype, dict) and inptype["type"] == "array":
             if inptype["items"] == "File":
                 action = cast(argparse.Action, FileAppendAction)
@@ -328,6 +348,7 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
     else:
         jobloaderctx = {
                 u"path": {u"@type": u"@id"},
+                u"location": {u"@type": u"@id"},
                 u"format": {u"@type": u"@id"},
                 u"id": u"@id"}
         jobloaderctx.update(t.metadata.get("$namespaces", {}))
@@ -396,6 +417,15 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
                   basedir=u"file://%s/" % input_basedir)
         return 0
 
+    def pathToLoc(p):
+        if "location" not in p:
+            p["location"] = p["path"]
+            del p["path"]
+
+    adjustDirObjs(job_order_object, pathToLoc)
+    adjustFileObjs(job_order_object, pathToLoc)
+    adjustDirObjs(job_order_object, functools.partial(getListing, StdFsAccess(input_basedir)))
+
     if "cwl:tool" in job_order_object:
         del job_order_object["cwl:tool"]
     if "id" in job_order_object:
@@ -404,32 +434,34 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
     return (job_order_object, input_basedir)
 
 
-def printdeps(obj, document_loader, stdout, relative_deps, basedir=None):
+def printdeps(obj, document_loader, stdout, relative_deps, uri, basedir=None):
     # type: (Dict[unicode, Any], Loader, IO[Any], bool, str) -> None
     deps = {"class": "File",
-            "path": obj.get("id", "#")}
+            "location": uri}
 
     def loadref(b, u):
         return document_loader.resolve_ref(u, base_url=b)[0]
 
-    sf = process.scandeps(basedir if basedir else obj["id"], obj,
+    sf = scandeps(basedir if basedir else uri, obj,
                           set(("$import", "run")),
-                          set(("$include", "$schemas", "path")), loadref)
+                          set(("$include", "$schemas", "path", "location")), loadref)
     if sf:
         deps["secondaryFiles"] = sf
 
     if relative_deps:
         if relative_deps == "primary":
-            base = basedir if basedir else os.path.dirname(obj["id"])
+            base = basedir if basedir else os.path.dirname(uri)
         elif relative_deps == "cwd":
             base = "file://" + os.getcwd()
         else:
             raise Exception(u"Unknown relative_deps %s" % relative_deps)
-        def makeRelative(u):
+        def makeRelative(ob):
+            u = ob.get("location", ob.get("path"))
             if ":" in u.split("/")[0] and not u.startswith("file://"):
-                return u
-            return os.path.relpath(u, base)
-        process.adjustFiles(deps, makeRelative)
+                pass
+            else:
+                ob["location"] = os.path.relpath(u, base)
+        adjustFileObjs(deps, makeRelative)
 
     stdout.write(json.dumps(deps, indent=4))
 
@@ -473,7 +505,7 @@ def print_pack(document_loader, processobj, uri, metadata):
     def loadref(b, u):
         # type: (unicode, unicode) -> Union[Dict, List, unicode]
         return document_loader.resolve_ref(u, base_url=b)[0]
-    deps = process.scandeps(uri, processobj,
+    deps = scandeps(uri, processobj,
                             set(("run",)), set(), loadref)
 
     fdeps = set((uri,))
@@ -583,7 +615,7 @@ def main(argsl=None,
             document_loader, workflowobj, uri = fetch_document(args.workflow)
 
             if args.print_deps:
-                printdeps(workflowobj, document_loader, stdout, args.relative_deps)
+                printdeps(workflowobj, document_loader, stdout, args.relative_deps, uri)
                 return 0
 
             document_loader, avsc_names, processobj, metadata, uri \
@@ -654,7 +686,8 @@ def main(argsl=None,
 
         if args.cachedir:
             setattr(args, 'cachedir', os.path.abspath(args.cachedir))
-            setattr(args, 'move_outputs', False)
+            if args.move_outputs == "move":
+                setattr(args, 'move_outputs', "copy")
 
         try:
             setattr(args, 'tmp_outdir_prefix',
@@ -666,8 +699,16 @@ def main(argsl=None,
                            makeTool=makeTool,
                            select_resources=selectResources,
                            **vars(args))
+
             # This is the workflow output, it needs to be written
             if out is not None:
+                def locToPath(p):
+                    if p["location"].startswith("file://"):
+                        p["path"] = p["location"][7:]
+
+                adjustDirObjs(out, locToPath)
+                adjustFileObjs(out, locToPath)
+
                 if isinstance(out, basestring):
                     stdout.write(out)
                 else:
diff --git a/cwltool/pathmapper.py b/cwltool/pathmapper.py
index 31b0be8bc..8455d648a 100644
--- a/cwltool/pathmapper.py
+++ b/cwltool/pathmapper.py
@@ -2,10 +2,49 @@
 import random
 import logging
 import stat
+import collections
 from typing import Tuple, Set, Union, Any
 
 _logger = logging.getLogger("cwltool")
 
+MapperEnt = collections.namedtuple("MapperEnt", ("resolved", "target", "type"))
+
+def adjustFiles(rec, op):  # type: (Any, Callable[..., Any]) -> None
+    """Apply a mapping function to each File path in the object `rec`."""
+
+    if isinstance(rec, dict):
+        if rec.get("class") == "File":
+            rec["path"] = op(rec["path"])
+        for d in rec:
+            adjustFiles(rec[d], op)
+    if isinstance(rec, list):
+        for d in rec:
+            adjustFiles(d, op)
+
+def adjustFileObjs(rec, op):  # type: (Any, Callable[[Any], Any]) -> None
+    """Apply an update function to each File object in the object `rec`."""
+
+    if isinstance(rec, dict):
+        if rec.get("class") == "File":
+            op(rec)
+        for d in rec:
+            adjustFileObjs(rec[d], op)
+    if isinstance(rec, list):
+        for d in rec:
+            adjustFileObjs(d, op)
+
+def adjustDirObjs(rec, op):  # type: (Any, Callable[[Any], Any]) -> None
+    """Apply an update function to each Directory object in the object `rec`."""
+
+    if isinstance(rec, dict):
+        if rec.get("class") == "Directory":
+            op(rec)
+        for d in rec:
+            adjustDirObjs(rec[d], op)
+    if isinstance(rec, list):
+        for d in rec:
+            adjustDirObjs(d, op)
+
 
 def abspath(src, basedir):  # type: (unicode, unicode) -> unicode
     if src.startswith(u"file://"):
@@ -20,22 +59,83 @@ class PathMapper(object):
     """Mapping of files from relative path provided in the file to a tuple of
     (absolute local path, absolute container path)"""
 
-    def __init__(self, referenced_files, basedir):
-        # type: (Set[unicode], unicode) -> None
+    def __init__(self, referenced_files, basedir, stagedir, separateDirs=True):
+        # type: (Set[Any], unicode, unicode) -> None
         self._pathmap = {}  # type: Dict[unicode, Tuple[unicode, unicode]]
+        self.stagedir = stagedir
+        self.separateDirs = separateDirs
         self.setup(referenced_files, basedir)
 
+    def visitlisting(self, listing, stagedir, basedir):
+        for ld in listing:
+            if "entryname" in ld:
+                tgt = os.path.join(stagedir, ld["entryname"])
+                if isinstance(ld["entry"], (str, unicode)):
+                    self._pathmap[str(id(ld["entry"]))] = MapperEnt(ld["entry"], tgt, "CreateFile")
+                else:
+                    if ld["entry"]["class"] == "Directory":
+                        self.visit(ld["entry"], tgt, basedir, copy=ld.get("writable", False))
+                    else:
+                        self.visit(ld["entry"], stagedir, basedir, entryname=ld["entryname"], copy=ld.get("writable", False))
+                    #ab = ld["entry"]["location"]
+                    #if ab.startswith("file://"):
+                    #    ab = ab[7:]
+                    #self._pathmap[ld["entry"]["location"]] = MapperEnt(ab, tgt, ld["entry"]["class"])
+            elif ld.get("class") == "File":
+                self.visit(ld, stagedir, basedir, copy=ld.get("writable", False))
+
+    def visit(self, obj, stagedir, basedir, entryname=None, copy=False):
+        if obj["class"] == "Directory":
+            if "location" in obj:
+                self._pathmap[obj["location"]] = MapperEnt(obj["location"], stagedir, "Directory")
+            else:
+                self._pathmap[str(id(obj))] = MapperEnt(str(id(obj)), stagedir, "Directory")
+            self.visitlisting(obj.get("listing", []), stagedir, basedir)
+        elif obj["class"] == "File":
+            path = obj["location"]
+            if path in self._pathmap:
+                return
+            ab = abspath(path, basedir)
+            if entryname:
+                tgt = os.path.join(stagedir, entryname)
+            else:
+                tgt = os.path.join(stagedir, os.path.basename(path))
+            if copy:
+                self._pathmap[path] = MapperEnt(ab, tgt, "WritableFile")
+            else:
+                self._pathmap[path] = MapperEnt(ab, tgt, "File")
+            self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
+
     def setup(self, referenced_files, basedir):
-        # type: (Set[unicode], unicode) -> None
-        for src in referenced_files:
-            ab = abspath(src, basedir)
-            self._pathmap[src] = (ab, ab)
+        # type: (Set[Any], unicode) -> None
+
+        # Go through each file and set the target to its own directory along
+        # with any secondary files.
+        stagedir = self.stagedir
+        for fob in referenced_files:
+            if self.separateDirs:
+                stagedir = os.path.join(self.stagedir, "stg%x" % random.randint(1, 1000000000))
+            self.visit(fob, stagedir, basedir)
+
+        # Dereference symbolic links
+        for path, (ab, tgt, type) in self._pathmap.items():
+            if type != "File": # or not os.path.exists(ab):
+                continue
+            deref = ab
+            st = os.lstat(deref)
+            while stat.S_ISLNK(st.st_mode):
+                rl = os.readlink(deref)
+                deref = rl if os.path.isabs(rl) else os.path.join(
+                        os.path.dirname(deref), rl)
+                st = os.lstat(deref)
+
+            self._pathmap[path] = MapperEnt(deref, tgt, "File")
 
     def mapper(self, src):  # type: (unicode) -> Tuple[unicode, unicode]
         if u"#" in src:
             i = src.index(u"#")
             p = self._pathmap[src[:i]]
-            return (p[0], p[1] + src[i:])
+            return (p.resolved, p.target + src[i:])
         else:
             return self._pathmap[src]
 
@@ -50,58 +150,3 @@ def reversemap(self, target):  # type: (unicode) -> Tuple[unicode, unicode]
             if v[1] == target:
                 return (k, v[0])
         return None
-
-
-class DockerPathMapper(PathMapper):
-
-    def __init__(self, referenced_files, basedir):
-        # type: (Set[unicode], unicode) -> None
-        self.dirs = {}  # type: Dict[unicode, Union[bool, unicode]]
-        super(DockerPathMapper, self).__init__(referenced_files, basedir)
-
-    def setup(self, referenced_files, basedir):
-        for src in referenced_files:
-            ab = abspath(src, basedir)
-            dirn, fn = os.path.split(ab)
-
-            subdir = False
-            for d in self.dirs:
-                if dirn.startswith(d):
-                  subdir = True
-                  break
-
-            if not subdir:
-                for d in list(self.dirs):
-                    if d.startswith(dirn):
-                        # 'dirn' is a parent of 'd'
-                        del self.dirs[d]
-                self.dirs[dirn] = True
-
-        prefix = u"job" + str(random.randint(1, 1000000000)) + u"_"
-
-        names = set()  # type: Set[unicode]
-        for d in self.dirs:
-            name = os.path.join(u"/var/lib/cwl", prefix + os.path.basename(d))
-            i = 1
-            while name in names:
-                i += 1
-                name = os.path.join(u"/var/lib/cwl",
-                        prefix + os.path.basename(d) + unicode(i))
-            names.add(name)
-            self.dirs[d] = name
-
-        for src in referenced_files:
-            ab = abspath(src, basedir)
-
-            deref = ab
-            st = os.lstat(deref)
-            while stat.S_ISLNK(st.st_mode):
-                rl = os.readlink(deref)
-                deref = rl if os.path.isabs(rl) else os.path.join(
-                        os.path.dirname(deref), rl)
-                st = os.lstat(deref)
-
-            for d in self.dirs:
-                if ab.startswith(d):
-                    self._pathmap[src] = (deref, os.path.join(
-                        self.dirs[d], ab[len(d)+1:]))
diff --git a/cwltool/process.py b/cwltool/process.py
index 98e35cf52..ea708c36c 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -1,45 +1,50 @@
-import abc
-import avro.schema
+
 import os
 import json
-import schema_salad.validate as validate
 import copy
 import logging
 import pprint
-from .utils import aslist, get_feature
-import schema_salad.schema
-from schema_salad.ref_resolver import Loader
-import urlparse
-import pprint
-from pkg_resources import resource_stream
 import stat
-from .builder import Builder, adjustFileObjs
 import tempfile
 import glob
-from .errors import WorkflowException, UnsupportedRequirement
-from .pathmapper import abspath
+import urlparse
+import pprint
+from collections import Iterable
+import errno
+import random
+import shutil
+
+import abc
+import schema_salad.validate as validate
+import schema_salad.schema
+from schema_salad.ref_resolver import Loader
+import avro.schema
 from typing import (Any, AnyStr, Callable, cast, Dict, List, Generator, IO,
         Tuple, Union)
-from collections import Iterable
 from rdflib import URIRef
 from rdflib.namespace import RDFS, OWL
-from .stdfsaccess import StdFsAccess
-import errno
 from rdflib import Graph
+from pkg_resources import resource_stream
+
+from .utils import aslist, get_feature
+from .stdfsaccess import StdFsAccess
+from .builder import Builder, adjustFileObjs, adjustDirObjs
+from .errors import WorkflowException, UnsupportedRequirement
+from .pathmapper import PathMapper, abspath
 
 _logger = logging.getLogger("cwltool")
 
 supportedProcessRequirements = ["DockerRequirement",
                                 "SchemaDefRequirement",
                                 "EnvVarRequirement",
-                                "CreateFileRequirement",
                                 "ScatterFeatureRequirement",
                                 "SubworkflowFeatureRequirement",
                                 "MultipleInputFeatureRequirement",
                                 "InlineJavascriptRequirement",
                                 "ShellCommandRequirement",
                                 "StepInputExpressionRequirement",
-                                "ResourceRequirement"]
+                                "ResourceRequirement",
+                                "InitialWorkDirRequirement"]
 
 cwl_files = ("Workflow.yml",
               "CommandLineTool.yml",
@@ -74,6 +79,8 @@
 
 SCHEMA_CACHE = {}  # type: Dict[str, Tuple[Loader, Union[avro.schema.Names, avro.schema.SchemaParseException], Dict[unicode, Any], Loader]]
 SCHEMA_FILE = None  # type: Dict[unicode, Any]
+SCHEMA_DIR = None  # type: Dict[unicode, Any]
+SCHEMA_DIRENT = None  # type: Dict[unicode, Any]
 SCHEMA_ANY = None  # type: Dict[unicode, Any]
 
 def get_schema(version):
@@ -106,19 +113,13 @@ def get_schema(version):
     SCHEMA_CACHE[version] = schema_salad.schema.load_schema(
         "https://w3id.org/cwl/CommonWorkflowLanguage.yml", cache=cache)
 
-    global SCHEMA_FILE, SCHEMA_ANY  # pylint: disable=global-statement
-    SCHEMA_FILE = cast(Dict[unicode, Any],
-            SCHEMA_CACHE[version][3].idx["https://w3id.org/cwl/cwl#File"])
-    SCHEMA_ANY = cast(Dict[unicode, Any],
-            SCHEMA_CACHE[version][3].idx["https://w3id.org/cwl/salad#Any"])
-
     return SCHEMA_CACHE[version]
 
 def shortname(inputid):
     # type: (unicode) -> unicode
     d = urlparse.urlparse(inputid)
     if d.fragment:
-        return d.fragment.split(u"/")[-1].split(u".")[-1]
+        return d.fragment.split(u"/")[-1]
     else:
         return d.path.split(u"/")[-1]
 
@@ -135,18 +136,6 @@ def checkRequirements(rec, supportedProcessRequirements):
         for d in rec:
             checkRequirements(d, supportedProcessRequirements)
 
-def adjustFiles(rec, op):  # type: (Any, Callable[..., Any]) -> None
-    """Apply a mapping function to each File path in the object `rec`."""
-
-    if isinstance(rec, dict):
-        if rec.get("class") == "File":
-            rec["path"] = op(rec["path"])
-        for d in rec:
-            adjustFiles(rec[d], op)
-    if isinstance(rec, list):
-        for d in rec:
-            adjustFiles(d, op)
-
 def adjustFilesWithSecondary(rec, op, primary=None):
     """Apply a mapping function to each File path in the object `rec`, propagating
     the primary file associated with a group of secondary files.
@@ -164,6 +153,80 @@ def adjustFilesWithSecondary(rec, op, primary=None):
         for d in rec:
             adjustFilesWithSecondary(d, op, primary)
 
+def getListing(fs_access, rec):
+    if "listing" not in rec:
+        listing = []
+        loc = rec["location"]
+        for ld in fs_access.listdir(loc):
+            if fs_access.isdir(ld):
+                ent = {"class": "Directory",
+                       "location": ld}
+                getListing(fs_access, ent)
+                listing.append({"entryname": os.path.basename(ld),
+                                 "entry": ent})
+            else:
+                listing.append({"entryname": os.path.basename(ld),
+                                 "entry": {"class": "File", "location": ld}})
+        rec["listing"] = listing
+
+def stageFiles(pm, stageFunc):
+    for f, p in pm.items():
+        if not os.path.exists(os.path.dirname(p.target)):
+            os.makedirs(os.path.dirname(p.target), 0755)
+        if p.type == "File":
+            stageFunc(p.resolved, p.target)
+        elif p.type == "WritableFile":
+            shutil.copy(p.resolved, p.target)
+        elif p.type == "CreateFile":
+            with open(p.target, "w") as n:
+                n.write(p.resolved.encode("utf-8"))
+
+def collectFilesAndDirs(obj, out):
+    if isinstance(obj, dict):
+        if obj.get("class") in ("File", "Directory"):
+            out.append(obj)
+        else:
+            for v in obj.values():
+                collectFilesAndDirs(v, out)
+    if isinstance(obj, list):
+        for l in obj:
+            collectFilesAndDirs(l, out)
+
+def relocateOutputs(outputObj, outdir, output_dirs, action):
+    if action not in ("move", "copy"):
+        return outputObj
+
+    def moveIt(src, dst):
+        for a in output_dirs:
+            if src.startswith(a):
+                if action == "move":
+                    _logger.debug("Moving %s to %s", src, dst)
+                    shutil.move(src, dst)
+                elif action == "copy":
+                    _logger.debug("Copying %s to %s", src, dst)
+                    shutil.copy(src, dst)
+
+    outfiles = []
+    collectFilesAndDirs(outputObj, outfiles)
+    pm = PathMapper(outfiles, "", outdir, separateDirs=False)
+    stageFiles(pm, moveIt)
+
+    def _check_adjust(f):
+        f["location"] = "file://" + pm.mapper(f["location"])[1]
+        return f
+
+    adjustFileObjs(outputObj, _check_adjust)
+    adjustDirObjs(outputObj, _check_adjust)
+
+    return outputObj
+
+def cleanIntermediate(output_dirs):
+    for a in output_dirs:
+        if os.path.exists(a) and empty_subtree(a):
+            _logger.debug(u"Removing intermediate output directory %s", a)
+            shutil.rmtree(a, True)
+
+
 def formatSubclassOf(fmt, cls, ontology, visited):
     # type: (str, str, Graph, Set[str]) -> bool
     """Determine if `fmt` is a subclass of `cls`."""
@@ -244,8 +307,21 @@ def __init__(self, toolpath_object, **kwargs):
         # type: (Dict[unicode, Any], **Any) -> None
         self.metadata = kwargs.get("metadata", {})  # type: Dict[str,Any]
         self.names = None  # type: avro.schema.Names
-        names = schema_salad.schema.make_avro_schema(
-            [SCHEMA_FILE, SCHEMA_ANY], schema_salad.ref_resolver.Loader({}))[0]
+
+        if SCHEMA_FILE is None:
+            global SCHEMA_FILE, SCHEMA_DIR, SCHEMA_DIRENT, SCHEMA_ANY  # pylint: disable=global-statement
+            get_schema("draft-4")
+            SCHEMA_ANY = cast(Dict[unicode, Any],
+                    SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/salad#Any"])
+            SCHEMA_FILE = cast(Dict[unicode, Any],
+                    SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#File"])
+            SCHEMA_DIR = cast(Dict[unicode, Any],
+                              SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#Directory"])
+            SCHEMA_DIRENT = cast(Dict[unicode, Any],
+                                 SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#Dirent"])
+
+        names = schema_salad.schema.make_avro_schema([SCHEMA_FILE, SCHEMA_DIR, SCHEMA_DIRENT, SCHEMA_ANY],
+                                                     schema_salad.ref_resolver.Loader({}))[0]
         if isinstance(names, avro.schema.SchemaParseException):
             raise names
         else:
@@ -333,13 +409,19 @@ def _init_job(self, joborder, **kwargs):
         builder.resources = {}
         builder.timeout = kwargs.get("eval_timeout")
 
-        dockerReq, _ = self.get_requirement("DockerRequirement")
+        dockerReq, is_req = self.get_requirement("DockerRequirement")
+
+        if dockerReq and is_req and not kwargs.get("use_container"):
+            raise WorkflowException("Document has DockerRequirement under 'requirements' but use_container is false.  DockerRequirement must be under 'hints' or use_container must be true.")
+
         if dockerReq and kwargs.get("use_container"):
             builder.outdir = kwargs.get("docker_outdir") or "/var/spool/cwl"
             builder.tmpdir = kwargs.get("docker_tmpdir") or "/tmp"
+            builder.stagedir = kwargs.get("docker_stagedir") or "/var/lib/cwl"
         else:
             builder.outdir = kwargs.get("outdir") or tempfile.mkdtemp()
             builder.tmpdir = kwargs.get("tmpdir") or tempfile.mkdtemp()
+            builder.stagedir = kwargs.get("stagedir") or tempfile.mkdtemp()
 
         builder.fs_access = kwargs.get("fs_access") or StdFsAccess(kwargs["basedir"])
 
@@ -369,6 +451,12 @@ def _init_job(self, joborder, **kwargs):
                     a["do_eval"] = a["valueFrom"]
                     a["valueFrom"] = None
                     builder.bindings.append(a)
+                elif ("$(" in a) or ("${" in a):
+                    builder.bindings.append({
+                        "position": [0, i],
+                        "do_eval": a,
+                        "valueFrom": None
+                    })
                 else:
                     builder.bindings.append({
                         "position": [0, i],
@@ -475,6 +563,41 @@ def uniquename(stem):  # type: (unicode) -> unicode
     _names.add(u)
     return u
 
+def nestdir(base, deps):
+    dirname = os.path.dirname(base) + "/"
+    subid = deps["location"]
+    if subid.startswith(dirname):
+        s2 = subid[len(dirname):]
+        sp = s2.split('/')
+        sp.pop()
+        while sp:
+            nx = sp.pop()
+            deps = {
+                "entryname": nx,
+                "entry": {
+                    "class": "Directory",
+                    "listing": [deps]
+                }
+            }
+    return deps
+
+def mergedirs(listing):
+    r = []
+    ents = {}
+    for e in listing:
+        if "entryname" in e:
+            if e["entryname"] not in ents:
+                ents[e["entryname"]] = e
+            elif e["entry"]["class"] == "Directory":
+                ents[e["entryname"]]["entry"]["listing"].extend(e["entry"]["listing"])
+        else:
+            r.append(e)
+    for e in ents.itervalues():
+        if e["entry"]["class"] == "Directory":
+            e["entry"]["listing"] = mergedirs(e["entry"]["listing"])
+    r.extend(ents.itervalues())
+    return r
+
 def scandeps(base, doc, reffields, urlfields, loadref):
     # type: (unicode, Any, Set[str], Set[str], Callable[[unicode, str], Any]) -> List[Dict[str, str]]
     r = []
@@ -485,7 +608,7 @@ def scandeps(base, doc, reffields, urlfields, loadref):
                 if base != df:
                     r.append({
                         "class": "File",
-                        "path": df
+                        "location": df
                     })
                     base = df
 
@@ -499,21 +622,26 @@ def scandeps(base, doc, reffields, urlfields, loadref):
                         subid = urlparse.urljoin(base, u)
                         deps = {
                             "class": "File",
-                            "path": subid
-                            }  # type: Dict[str, Any]
+                            "location": subid
+                        }  # type: Dict[str, Any]
                         sf = scandeps(subid, sub, reffields, urlfields, loadref)
                         if sf:
                             deps["secondaryFiles"] = sf
+                        deps = nestdir(base, deps)
                         r.append(deps)
             elif k in urlfields:
                 for u in aslist(v):
-                    r.append({
+                    deps = {
                         "class": "File",
-                        "path": urlparse.urljoin(base, u)
-                    })
+                        "location": urlparse.urljoin(base, u)
+                    }
+                    deps = nestdir(base, deps)
+                    r.append(deps)
             else:
                 r.extend(scandeps(base, v, reffields, urlfields, loadref))
     elif isinstance(doc, list):
         for d in doc:
             r.extend(scandeps(base, d, reffields, urlfields, loadref))
+
+    r = mergedirs(r)
     return r
diff --git a/cwltool/schemas/draft-3/examples/arguments.cwl b/cwltool/schemas/draft-3/examples/arguments.cwl
index 862540be2..23e91ebdd 100644
--- a/cwltool/schemas/draft-3/examples/arguments.cwl
+++ b/cwltool/schemas/draft-3/examples/arguments.cwl
@@ -1,5 +1,6 @@
 cwlVersion: cwl:draft-3
 class: CommandLineTool
+label: Example trivial wrapper for Java 7 compiler
 baseCommand: javac
 hints:
   - class: DockerRequirement
diff --git a/cwltool/schemas/draft-4/CommandLineTool.yml b/cwltool/schemas/draft-4/CommandLineTool.yml
index cec579407..f33dadfc4 100644
--- a/cwltool/schemas/draft-4/CommandLineTool.yml
+++ b/cwltool/schemas/draft-4/CommandLineTool.yml
@@ -79,30 +79,6 @@ $graph:
     - {$include: concepts.md}
     - {$include: invocation.md}
 
-- type: record
-  name: FileDef
-  doc: |
-    Define a file that must be placed in the designated output directory
-    prior to executing the command line tool.  May be the result of executing
-    an expression, such as building a configuration file from a template.
-  fields:
-    - name: "filename"
-      type: ["string", "#Expression"]
-      doc: "The name of the file to create in the output directory."
-    - name: "fileContent"
-      type: ["string", "#Expression"]
-      doc: |
-        If the value is a string literal or an expression which evaluates to a
-        string, a new file must be created with the string as the file contents.
-
-        If the value is an expression that evaluates to a File object, this
-        indicates the referenced file should be added to the designated output
-        directory prior to executing the tool.
-
-        Files added in this way may be read-only, and may be provided
-        by bind mounts or file system links to avoid
-        unnecessary copying of the input file.
-
 
 - type: record
   name: EnvironmentDef
@@ -248,17 +224,6 @@ $graph:
         the File objects must include up to the first 64 KiB of file contents
         in the `contents` field.
 
-- name: initialWorkDir
-  type: record
-  doc: |
-    Setup a working directory based on a number of input files (and/or directories)
-  fields:
-    - name: dirDef
-      type:
-        type: "array"
-        items: [ "#FileDef", "#File", "#Directory" ]
-      doc: list of files and/or directories
-
 
 - name: CommandInputRecordField
   type: record
@@ -499,7 +464,7 @@ $graph:
       type:
         - "null"
         - type: array
-          items: [string, "#CommandLineBinding"]
+          items: [string, "#Expression", "#CommandLineBinding"]
       jsonldPredicate:
         "_id": "cwl:arguments"
         "_container": "@list"
@@ -626,21 +591,72 @@ $graph:
         Docker container.
 
 
-
-- name: CreateFileRequirement
+- name: DirentExt
   type: record
-  extends: "#ProcessRequirement"
   doc: |
-    Define a list of files that must be created by the workflow
-    platform in the designated output directory prior to executing the command
-    line tool.  See `FileDef` for details.
+    Define a file or subdirectory that must be placed in the designated output
+    directory prior to executing the command line tool.  May be the result of
+    executing an expression, such as building a configuration file from a
+    template.
   fields:
-    - name: fileDef
+    - name: entryname
+      type: [string, Expression]
+      jsonldPredicate:
+        _id: cwl:entryname
+      doc: |
+        The name of the file or subdirectory to create in the output directory.
+    - name: entry
+      type: [string, Expression]
+      jsonldPredicate:
+        _id: cwl:entry
+      doc: |
+        If the value is a string literal or an expression which evaluates to a
+        string, a new file must be created with the string as the file contents.
+
+        If the value is an expression that evaluates to a `File` object, this
+        indicates the referenced file should be added to the designated output
+        directory prior to executing the tool.
+
+        If the value is an expression that evaluates to a `Dirent` object, this
+        indicates that the File or Directory in `entry` should be added to the
+        designated output directory with the name in `entryname`.
+
+        If `writable` is false, the file may be made available using a bind
+        mount or file system link to avoid unnecessary copying of the input
+        file.
+    - name: writable
+      type: boolean?
+      doc: |
+        If true, the file or directory must be writable by the tool.  Changes
+        to the file or directory must be isolated and not visible by any other
+        CommandLineTool process.  This may be implemented by making a copy of
+        the original file or directory.  Default false (files and directories
+        read-only by default).
+
+- name: InitialWorkDirRequirement
+  type: record
+  extends: ProcessRequirement
+  doc:
+    Define a list of files and subdirectories that must be created by the
+    workflow platform in the designated output directory prior to executing the
+    command line tool.
+  fields:
+    - name: listing
       type:
-        type: "array"
-        items: "#FileDef"
-      doc: The list of files.
+        - type: array
+          items: [File, DirentExt]
+        - string
+        - Expression
+      jsonldPredicate:
+        _id: "cwl:listing"
+        mapSubject: entryname
+        mapPredicate: entry
+      doc: |
+        The list of files or subdirectories that must be placed in the
+        designated output directory prior to executing the command line tool.
 
+        May be an expression.  If so, the expression return value must validate
+        as `{type: array, items: [File, Dirent]}`.
 
 - name: EnvVarRequirement
   type: record
diff --git a/cwltool/schemas/draft-4/Process.yml b/cwltool/schemas/draft-4/Process.yml
index 319ff27f0..351bab9d2 100644
--- a/cwltool/schemas/draft-4/Process.yml
+++ b/cwltool/schemas/draft-4/Process.yml
@@ -33,15 +33,18 @@ $graph:
     - cwl:draft-3
     - cwl:draft-4.dev1
     - cwl:draft-4.dev2
+    - cwl:draft-4.dev3
 
 - name: CWLType
   type: enum
   extends: "sld:PrimitiveType"
   symbols:
     - cwl:File
+    - cwl:Directory
   doc:
     - "Extends primitive types with the concept of a file as a first class type."
     - "File: A File object"
+    - "Directory: A Directory object"
 
 - name: File
   type: record
@@ -58,20 +61,87 @@ $graph:
         symbols:
           - cwl:File
       jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
+        _id: "@type"
+        _type: "@vocab"
       doc: Must be `File` to indicate this object describes a file.
-    - name: path
+    - name: location
       type: string
-      doc: The path to the file.
+      doc: |
+        A URI that identifies the file resource.  This may be a relative
+        reference, in which case it must be resolved using the base URI of the
+        document.  The location may refer to a local or remote resource; the
+        implementation must use the URI to retrieve file content.  If an
+        implementation is unable to retrieve the file content stored at a
+        remote resource (due to unsupported protocol, access denied, or other
+        issue) it must signal an error.
+
+        If the `path` field is provided but the `location` field is not, an
+        implementation may assign the value of the `path` field to `location`,
+        then follow the rules above.
+      jsonldPredicate:
+        _id: "@id"
+        _type: "@id"
+    - name: path
+      type: string?
+      doc: |
+        The local path where the File is made available prior to executing a
+        CommandLineTool.  This must be set by the implementation.  This field
+        must not be used in any other context.  The command line tool being
+        executed must be able to to access the file at `path` using the POSIX
+        `open(2)` syscall.
       jsonldPredicate:
         "_id": "cwl:path"
         "_type": "@id"
+    - name: basename
+      type: string?
+      doc: |
+        The base name of the file, that is, the path component following the
+        final slash in the path.
+
+        The implementation must set this field based on the value of `path`
+        prior to evaluating parameter references or expressions in a
+        CommandLineTool document.  This field must not be used in any other
+        context.
+    - name: dirname
+      type: string?
+      doc: |
+        The name of the directory containing file, that is, the path leading up
+        to the final slash in the path such that `dirname + '/' + basename =
+        path`.
+
+        The implementation must set this field based on the value of `path`
+        prior to evaluating parameter references or expressions in a
+        CommandLineTool document.  This field must not be used in any other
+        context.
+    - name: nameroot
+      type: string?
+      doc: |
+        The basename root such that `nameroot + nameext == basename`, and
+        `nameext` is empty or begins with a period and contains at most one
+        period.  Leading periods on the basename are ignored; a basename of
+        `.cshrc` will have a nameroot of `.cshrc`.
+
+        The implementation must set this field based on the value of `path`
+        prior to evaluating parameter references or expressions in a
+        CommandLineTool document.  This field must not be used in any other
+        context.
+    - name: nameext
+      type: string?
+      doc: |
+        The basename extension such that `nameroot + nameext == basename`, and
+        `nameext` is empty or begins with a period and contains at most one
+        period.  Leading periods on the basename are ignored; a basename of
+        `.cshrc` will have an empty `nameext`.
+
+        The implementation must set this field based on the value of `path`
+        prior to evaluating parameter references or expressions in a
+        CommandLineTool document.  This field must not be used in any other
+        context.
     - name: checksum
       type: ["null", string]
       doc: |
         Optional hash code for validating file integrity.  Currently must be in the form
-        "sha1$ + hexidecimal string" using the SHA-1 algorithm.
+        "sha1$ + hexadecimal string" using the SHA-1 algorithm.
     - name: size
       type: ["null", long]
       doc: Optional file size.
@@ -79,7 +149,7 @@ $graph:
       type:
         - "null"
         - type: array
-          items: "#File"
+          items: [File, Dirent]
       jsonldPredicate: "cwl:secondaryFiles"
       doc: |
         A list of additional files that are associated with the primary file
@@ -111,12 +181,24 @@ $graph:
         runtime may perform exact file format matches.
 
 
+- name: Dirent
+  type: record
+  fields:
+    - name: entryname
+      type: string
+      jsonldPredicate:
+        "_id": cwl:entryname
+    - name: entry
+      type: [File, Directory]
+      jsonldPredicate:
+        "_id": cwl:entry
+
 - name: Directory
   type: record
   docParent: "#CWLType"
   doc: |
     Represents a directory to present to a command line tool. This could be a virtual
-    directory, made of files assembled from a number of concrete directories.
+    directory, made of files assembled from multiple locations.
   fields:
     - name: class
       type:
@@ -125,18 +207,48 @@ $graph:
         symbols:
           - cwl:Directory
       jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
+        _id: "@type"
+        _type: "@vocab"
       doc: Must be `Directory` to indicate this object describes a Directory.
-    - name: path
+    - name: location
       type: string
-      doc: The path to the directory.
+      doc: |
+        A URI that identifies the directory resource.  This may be a relative
+        reference, in which case it must be resolved using the base URI of the
+        document.  The location may refer to a local or remote resource.  If
+        the `listing` field is not set, the implementation must use the
+        location URI to retrieve directory listing.  If an implementation is
+        unable to retrieve the directory listing stored at a remote resource (due to
+        unsupported protocol, access denied, or other issue) it must signal an
+        error.
+
+        If the `path` field is provided but the `location` field is not, an
+        implementation may assign the value of the `path` field to `location`,
+        then follow the rules above.
       jsonldPredicate:
-        "_id": "cwl:path"
-        "_type": "@id"
-    # - name: size
-    #   type: ["null", long]
-    #   doc: Optional directory size.
+        _id: "@id"
+        _type: "@id"
+    - name: path
+      type: string?
+      doc: |
+        The local path where the Directory is made available prior to executing a
+        CommandLineTool.  This must be set by the implementation.  This field
+        must not be used in any other context.  The command line tool being
+        executed must be able to to access the directory at `path` using the POSIX
+        `opendir(2)` syscall.
+      jsonldPredicate:
+        _id: "cwl:path"
+        _type: "@id"
+    - name: listing
+      type:
+        - "null"
+        - type: array
+          items: [File, Dirent]
+      doc: List of files or subdirectories contained in this directory
+      jsonldPredicate:
+        _id: "cwl:listing"
+        mapSubject: entryname
+        mapPredicate: entry
 
 - name: SchemaBase
   type: record
diff --git a/cwltool/schemas/draft-4/conformance_test_draft-4.yaml b/cwltool/schemas/draft-4/conformance_test_draft-4.yaml
index ae839ba0a..7769640b8 100644
--- a/cwltool/schemas/draft-4/conformance_test_draft-4.yaml
+++ b/cwltool/schemas/draft-4/conformance_test_draft-4.yaml
@@ -40,7 +40,7 @@
     "foo": {
         "checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
         "class": "File",
-        "path": "foo.txt",
+        "location": "foo.txt",
         "size": 22
     }
   job: draft-4/cat-job.json
@@ -52,44 +52,61 @@
     output_file:
       class: File
       checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
-      path: output.txt
+      location: output.txt
       size: 13
   tool: draft-4/cat3-tool.cwl
   doc: Test command execution in Docker with stdout redirection
 
 - job: draft-4/cat-job.json
   tool: draft-4/cat3-tool-shortcut.cwl
-  doc: Test command execution in Docker with stdout redirection
+  output:
+    output_file:
+      class: File
+      checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
+      location:
+      size: 13
+  doc: Test command execution in Docker with simplified syntax stdout redirection
 
 - job: draft-4/cat-job.json
   output:
     output_file:
       class: File
       checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
-      path: cat-out
+      location: cat-out
       size: 13
   tool: draft-4/cat3-tool-mediumcut.cwl
   doc: Test command execution in Docker with stdout redirection
 
-- args: [egrep]
-  stderr: error.txt
-  job:
+- job:
+  output: {
+    "output_file": {
+        "checksum": "sha1$cec7b8746a78c42060c96505887449bca0142976",
+        "size": 84,
+        "location": "error.txt",
+        "class": "File"
+    }
+  }
   tool: draft-4/egrep-stderr.cwl
   doc: Test command line with stderr redirection
 
-- args: [egrep]
-  job:
+- job:
+  output: {
+    "output_file": {
+        "checksum": "sha1$cec7b8746a78c42060c96505887449bca0142976",
+        "size": 84,
+        "location": "",
+        "class": "File"
+    }
+  }
   tool: draft-4/egrep-stderr-shortcut.cwl
   doc: Test command line with stderr redirection, brief syntax
 
-- args: [egrep]
-  stderr: std.err
-  output:
+- output:
     output_file:
       class: File
       size: 84
       checksum: sha1$cec7b8746a78c42060c96505887449bca0142976
-      path: std.err
+      location: std.err
   job:
   tool: draft-4/egrep-stderr-mediumcut.cwl
   doc: Test command line with stderr redirection, named brief syntax
@@ -99,7 +116,7 @@
     output_txt:
       class: File
       checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
-      path: output.txt
+      location: output.txt
       size: 13
   tool: draft-4/cat4-tool.cwl
   doc: Test command execution in Docker with stdin and stdout redirection
@@ -144,7 +161,7 @@
     output:
       class: File
       checksum: sha1$631bfbac524e2d04cdcc5ec33ade827fc10b06ae
-      path: output
+      location: output
       size: 15
   tool: draft-4/wc-tool.cwl
   doc: Test command execution in with stdin and stdout redirection
@@ -214,7 +231,7 @@
     out:
       class: File
       checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
-      path: out
+      location: out
       size: 15
   tool: draft-4/env-tool1.cwl
   doc: Test EnvVarRequirement
@@ -259,7 +276,7 @@
     out:
       class: File
       checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
-      path: out
+      location: out
       size: 15
   tool: draft-4/env-wf1.cwl
   doc: Test requirement priority
@@ -269,7 +286,7 @@
     out:
       class: File
       checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6
-      path: out
+      location: out
       size: 9
   tool: draft-4/env-wf2.cwl
   doc: Test requirements override hints
@@ -284,7 +301,7 @@
     output:
       class: File
       checksum: sha1$b9214658cc453331b62c2282b772a5c063dbd284
-      path: output.txt
+      location: output.txt
       size: 1111
   tool: draft-4/revsort.cwl
   doc: Test sample workflows from the specification
@@ -294,7 +311,7 @@
     output_file:
       class: File
       checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
-      path: output.txt
+      location: output.txt
       size: 13
   tool: draft-4/cat5-tool.cwl
   doc: Test unknown hints are ignored.
@@ -304,32 +321,32 @@
     outfile:
       class: File
       checksum: sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0
-      path: result.txt
+      location: result.txt
       size: 142
     indexedfile: {
-        "path": "input.txt",
+        "location": "input.txt",
         "class": "File",
         "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
         "secondaryFiles": [
             {
-                "path": "input.txt.idx1",
-                "class": "File"
+                "location": "input.txt.idx1",
+                "class": "File",
             },
             {
-                "path": "input.idx2",
-                "class": "File"
+                "location": "input.idx2",
+                "class": "File",
             },
             {
-                "path": "input.txt.idx3",
-                "class": "File"
+                "location": "input.txt.idx3",
+                "class": "File",
             },
             {
-                "path": "input.txt.idx4",
-                "class": "File"
+                "location": "input.txt.idx4",
+                "class": "File",
             },
             {
-                "path": "input.txt.idx5",
-                "class": "File"
+                "location": "input.txt.idx5",
+                "class": "File",
             }
         ],
         "size": 1111
@@ -344,7 +361,7 @@
     outfile:
       class: File
       checksum: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
-      path: fish.txt
+      location: fish.txt
       size: 1111
   tool: draft-4/rename.cwl
   doc: |
@@ -360,7 +377,7 @@
 - job: draft-4/schemadef-job.json
   output:
     output:
-        path: output.txt
+        location: output.txt
         size: 12
         class: File
         checksum: "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e"
@@ -371,7 +388,7 @@
 - job: draft-4/schemadef-job.json
   output:
     output:
-        path: output.txt
+        location: output.txt
         size: 12
         class: File
         checksum: "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e"
@@ -537,7 +554,7 @@
 - job: draft-4/formattest-job.json
   output:
     output:
-        "path": "output.txt"
+        "location": "output.txt"
         "format": "http://edamontology.org/format_2330"
         "size": 1111
         "class": "File"
@@ -549,7 +566,7 @@
 - job: draft-4/formattest2-job.json
   output:
     output:
-        "path": "output.txt"
+        "location": "output.txt"
         "format": "http://edamontology.org/format_1929"
         "size": 12010
         "class": "File"
@@ -561,7 +578,7 @@
 - job: draft-4/formattest2-job.json
   output:
     output:
-        "path": "output.txt"
+        "location": "output.txt"
         "format": "http://edamontology.org/format_1929"
         "size": 12010
         "class": "File"
@@ -575,7 +592,7 @@
   output:
     optional_file: null
     output_file:
-        path: output.txt
+        location: output.txt
         size: 13
         class: "File"
         checksum: "sha1$47a013e660d408619d894b20806b1d5086aab03b"
@@ -601,13 +618,13 @@
   output:
     "orec": {
         "ofoo": {
-            "path": "foo",
+            "location": "foo",
             "size": 1111,
             "class": "File",
             "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"
         },
         "obar": {
-            "path": "bar",
+            "location": "bar",
             "size": 12010,
             "class": "File",
             "checksum": "sha1$aeb3d11bdf536511649129f4077d5cda6a324118"
@@ -619,7 +636,7 @@
 - job: draft-4/empty.json
   output: {
     "foo": {
-        "path": "foo",
+        "location": "foo",
         "class": "File"
     }
   }
@@ -629,19 +646,19 @@
 - job: draft-4/abc.json
   output:
     files: [{
-        "path": "a",
+        "location": "a",
         "size": 0,
         "class": "File",
         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
     },
     {
-        "path": "b",
+        "location": "b",
         "size": 0,
         "class": "File",
         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
     },
     {
-        "path": "c",
+        "location": "c",
         "size": 0,
         "class": "File",
         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"
@@ -676,7 +693,7 @@
 - job: draft-4/conflict-job.json
   output: {
     "fileout": {
-        "path": "out.txt",
+        "location": "out.txt",
         "checksum": "sha1$a2d8d6e7b28295dc9977dc3bdb652ddd480995f0",
         "class": "File",
         "size": 25
@@ -684,3 +701,73 @@
   }
   tool: "draft-4/conflict-wf.cwl#collision"
   doc: Test workflow two input files with same name.
+
+- job: draft-4/dir-job.yml
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592",
+        "class": "File"
+    }
+  tool: draft-4/dir.cwl
+  doc: Test directory input
+
+- job: draft-4/dir-job.yml
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592",
+        "class": "File"
+    }
+  tool: draft-4/dir2.cwl
+  doc: Test directory input in Docker
+
+- job: draft-4/dir3-job.yml
+  output:
+    "outdir": {
+        "class": "Directory",
+        "listing": [
+            {
+                "entryname": "hello.txt",
+                "entry": {
+                    "class": "File",
+                    "location": "hello.txt"
+                }
+            },
+            {
+                "entryname": "goodbye.txt",
+                "entry": {
+                    "class": "File",
+                    "location": "goodbye.txt"
+                }
+            }
+        ],
+    }
+  tool: draft-4/dir3.cwl
+  doc: Test directory input in Docker
+
+- job: draft-4/dir4-job.yml
+  output: {
+    "outlist": {
+        "checksum": "sha1$2ab6f189e84753c05a23413fbf6b6fbf4c53489f",
+        "size": 90,
+        "location": "output.txt",
+        "class": "File"
+    }
+  }
+  tool: draft-4/dir4.cwl
+  doc: Test directories in secondaryFiles
+
+- job: draft-4/dir-job.yml
+  output: {
+    "outlist": {
+        "checksum": "sha1$907a866a3e0b7f1fc5a2222531c5fb9063704438",
+        "size": 33,
+        "location": "output.txt",
+        "class": "File"
+    }
+  }
+  tool: draft-4/dir5.cwl
+  doc: Test dynamic initial work dir
diff --git a/cwltool/schemas/draft-4/draft-4/binding-test.cwl b/cwltool/schemas/draft-4/draft-4/binding-test.cwl
index 7e6c3c826..395c50a92 100755
--- a/cwltool/schemas/draft-4/draft-4/binding-test.cwl
+++ b/cwltool/schemas/draft-4/draft-4/binding-test.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   - id: reference
@@ -19,7 +19,7 @@ inputs:
     type: File
     default:
       class: File
-      path: args.py
+      location: args.py
     inputBinding:
       position: -1
 
diff --git a/cwltool/schemas/draft-4/draft-4/bwa-mem-job.json b/cwltool/schemas/draft-4/draft-4/bwa-mem-job.json
index 48d7d6cfe..f3e900dea 100644
--- a/cwltool/schemas/draft-4/draft-4/bwa-mem-job.json
+++ b/cwltool/schemas/draft-4/draft-4/bwa-mem-job.json
@@ -1,18 +1,18 @@
 {
     "reference": {
         "class": "File",
-        "path": "chr20.fa",
+        "location": "chr20.fa",
         "size": 123,
         "checksum": "sha1$hash"
     },
     "reads": [
         {
             "class": "File",
-            "path": "example_human_Illumina.pe_1.fastq"
+            "location": "example_human_Illumina.pe_1.fastq"
         },
         {
             "class": "File",
-            "path": "example_human_Illumina.pe_2.fastq"
+            "location": "example_human_Illumina.pe_2.fastq"
         }
     ],
     "min_std_max_min": [
diff --git a/cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl b/cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl
index b0722effa..63ecb885e 100755
--- a/cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: draft-4.dev2
+cwlVersion: draft-4.dev3
 
 class: CommandLineTool
 
@@ -34,7 +34,7 @@ inputs:
     type: File
     default:
       class: File
-      path: args.py
+      location: args.py
     inputBinding:
       position: -1
 
diff --git a/cwltool/schemas/draft-4/draft-4/cat-job.json b/cwltool/schemas/draft-4/draft-4/cat-job.json
index 09f16ba7b..837875d92 100644
--- a/cwltool/schemas/draft-4/draft-4/cat-job.json
+++ b/cwltool/schemas/draft-4/draft-4/cat-job.json
@@ -1,6 +1,6 @@
 {
     "file1": {
         "class": "File",
-        "path": "hello.txt"
+        "location": "hello.txt"
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/cat-n-job.json b/cwltool/schemas/draft-4/draft-4/cat-n-job.json
index ee6416857..1b93b815a 100644
--- a/cwltool/schemas/draft-4/draft-4/cat-n-job.json
+++ b/cwltool/schemas/draft-4/draft-4/cat-n-job.json
@@ -1,7 +1,7 @@
 {
     "file1": {
         "class": "File",
-        "path": "hello.txt"
+        "location": "hello.txt"
     },
     "numbering": true
 }
diff --git a/cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl b/cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl
index 3bad2b662..04c3857f6 100755
--- a/cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 {
     "class": "CommandLineTool",
-    "cwlVersion": "cwl:draft-4.dev2",
+    "cwlVersion": "cwl:draft-4.dev3",
     "description": "Print the contents of a file to stdout using 'cat' running in a docker container.",
     "inputs": [
         {
@@ -22,7 +22,7 @@
         type: File,
         default: {
           class: File,
-          path: args.py
+          location: args.py
         },
         inputBinding: {
           position: -1
diff --git a/cwltool/schemas/draft-4/draft-4/cat1-tool.cwl b/cwltool/schemas/draft-4/draft-4/cat1-tool.cwl
index 8c7402f33..2ccde1553 100755
--- a/cwltool/schemas/draft-4/draft-4/cat1-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat1-tool.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
diff --git a/cwltool/schemas/draft-4/draft-4/cat2-tool.cwl b/cwltool/schemas/draft-4/draft-4/cat2-tool.cwl
index 8038f5163..8348a82f5 100755
--- a/cwltool/schemas/draft-4/draft-4/cat2-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat2-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl b/cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl
index 1c29102eb..2e3f7282a 100755
--- a/cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl b/cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl
index 4d12a4df4..04eb14d5e 100755
--- a/cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/cat3-tool.cwl b/cwltool/schemas/draft-4/draft-4/cat3-tool.cwl
index 56df0f6f8..f67588a9b 100755
--- a/cwltool/schemas/draft-4/draft-4/cat3-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat3-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/cat4-tool.cwl b/cwltool/schemas/draft-4/draft-4/cat4-tool.cwl
index 1fefd2cf9..733bc9167 100755
--- a/cwltool/schemas/draft-4/draft-4/cat4-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat4-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/cat5-tool.cwl b/cwltool/schemas/draft-4/draft-4/cat5-tool.cwl
index f7010e4a8..24e89d91d 100755
--- a/cwltool/schemas/draft-4/draft-4/cat5-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/cat5-tool.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
diff --git a/cwltool/schemas/draft-4/draft-4/conflict-wf.cwl b/cwltool/schemas/draft-4/draft-4/conflict-wf.cwl
index 2e197004d..c72b27bf2 100644
--- a/cwltool/schemas/draft-4/draft-4/conflict-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/conflict-wf.cwl
@@ -1,4 +1,4 @@
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 $graph:
 - id: echo
   class: CommandLineTool
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl
index 96244ec2b..7c58ec84f 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   file1:
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl
index 65c1fc1d3..267f949ba 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   InlineJavascriptRequirement: {}
 
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines3-job.json b/cwltool/schemas/draft-4/draft-4/count-lines3-job.json
index 3bdd5a322..3a93e32d4 100644
--- a/cwltool/schemas/draft-4/draft-4/count-lines3-job.json
+++ b/cwltool/schemas/draft-4/draft-4/count-lines3-job.json
@@ -2,11 +2,11 @@
     "file1": [
         {
             "class": "File",
-            "path": "whale.txt"
+            "location": "whale.txt"
         },
         {
             "class": "File",
-            "path": "hello.txt"
+            "location": "hello.txt"
         }
     ]
 }
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl
index f7cde5a31..d48cd9258 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     file1:
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines4-job.json b/cwltool/schemas/draft-4/draft-4/count-lines4-job.json
index dcd309a6e..1c85bea01 100644
--- a/cwltool/schemas/draft-4/draft-4/count-lines4-job.json
+++ b/cwltool/schemas/draft-4/draft-4/count-lines4-job.json
@@ -1,10 +1,10 @@
 {
     "file1": {
         "class": "File",
-        "path": "whale.txt"
+        "location": "whale.txt"
     },
     "file2": {
         "class": "File",
-        "path": "hello.txt"
+        "location": "hello.txt"
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl
index 4c73d480c..8aada50e3 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     file1:
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl
index 2af0f8597..eb38e2231 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl
@@ -1,11 +1,11 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     file1:
       type: File
-      default: {class: File, path: hello.txt}
+      default: {class: File, location: hello.txt}
 outputs:
     count_output:
       type: int
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines6-job.json b/cwltool/schemas/draft-4/draft-4/count-lines6-job.json
index 4db2d1d70..3652ded9d 100644
--- a/cwltool/schemas/draft-4/draft-4/count-lines6-job.json
+++ b/cwltool/schemas/draft-4/draft-4/count-lines6-job.json
@@ -2,21 +2,21 @@
     "file1": [
         {
             "class": "File",
-            "path": "whale.txt"
+            "location": "whale.txt"
         },
         {
             "class": "File",
-            "path": "whale.txt"
+            "location": "whale.txt"
         }
     ],
     "file2": [
         {
             "class": "File",
-            "path": "hello.txt"
+            "location": "hello.txt"
         },
         {
             "class": "File",
-            "path": "hello.txt"
+            "location": "hello.txt"
         }
     ]
 }
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl
index 69accb422..36296bffa 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     file1: File[]
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl
index 1394fcf1e..cf0e3d8dd 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 requirements:
   - class: MultipleInputFeatureRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl
index f743718fb..02895b549 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     file1: File
diff --git a/cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl b/cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl
index aff39fcb8..9a340adc6 100755
--- a/cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs: []
 
@@ -16,7 +16,7 @@ steps:
       file1:
         default:
           class: File
-          path: whale.txt
+          location: whale.txt
     out: [output]
 
   step2:
diff --git a/cwltool/schemas/draft-4/draft-4/dir-job.yml b/cwltool/schemas/draft-4/draft-4/dir-job.yml
new file mode 100644
index 000000000..30392cfc0
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir-job.yml
@@ -0,0 +1,3 @@
+indir:
+  class: Directory
+  location: testdir
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/dir.cwl b/cwltool/schemas/draft-4/draft-4/dir.cwl
new file mode 100644
index 000000000..0cfe978e8
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir.cwl
@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+requirements:
+  - class: ShellCommandRequirement
+inputs:
+  indir: Directory
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: []
+arguments: ["cd", "$(inputs.indir.path)",
+  {shellQuote: false, valueFrom: "&&"},
+  "find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/dir2.cwl b/cwltool/schemas/draft-4/draft-4/dir2.cwl
new file mode 100644
index 000000000..e64af2c7b
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir2.cwl
@@ -0,0 +1,20 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+hints:
+  DockerRequirement:
+    dockerPull: debian:8
+  ShellCommandRequirement: {}
+inputs:
+  indir: Directory
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: []
+arguments: ["cd", "$(inputs.indir.path)",
+  {shellQuote: false, valueFrom: "&&"},
+  "find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/dir3-job.yml b/cwltool/schemas/draft-4/draft-4/dir3-job.yml
new file mode 100644
index 000000000..aff0e8036
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir3-job.yml
@@ -0,0 +1,3 @@
+inf:
+  class: File
+  location: hello.tar
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/dir3.cwl b/cwltool/schemas/draft-4/draft-4/dir3.cwl
new file mode 100644
index 000000000..61fb96eba
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir3.cwl
@@ -0,0 +1,13 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+baseCommand: [tar, xvf]
+inputs:
+  inf:
+    type: File
+    inputBinding:
+      position: 1
+outputs:
+  outdir:
+    type: Directory
+    outputBinding:
+      glob: .
diff --git a/cwltool/schemas/draft-4/draft-4/dir4-job.yml b/cwltool/schemas/draft-4/draft-4/dir4-job.yml
new file mode 100644
index 000000000..8da860d27
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir4-job.yml
@@ -0,0 +1,10 @@
+inf:
+  class: File
+  location: hello.tar
+  secondaryFiles:
+    - class: File
+      location: index.py
+    - entryname: xtestdir
+      entry:
+        class: Directory
+        location: testdir
diff --git a/cwltool/schemas/draft-4/draft-4/dir4.cwl b/cwltool/schemas/draft-4/draft-4/dir4.cwl
new file mode 100644
index 000000000..07341cf7d
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir4.cwl
@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+requirements:
+  - class: ShellCommandRequirement
+inputs:
+  inf: File
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: []
+arguments: ["cd", "$(inputs.inf.dirname)",
+  {shellQuote: false, valueFrom: "&&"},
+  "find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/dir5.cwl b/cwltool/schemas/draft-4/draft-4/dir5.cwl
new file mode 100644
index 000000000..27d9ac9e9
--- /dev/null
+++ b/cwltool/schemas/draft-4/draft-4/dir5.cwl
@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+requirements:
+  - class: ShellCommandRequirement
+  - class: InitialWorkDirRequirement
+    listing: $(inputs.indir.listing)
+inputs:
+  indir: Directory
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: []
+arguments: ["find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/echo-tool.cwl b/cwltool/schemas/draft-4/draft-4/echo-tool.cwl
index 85c113939..f207942ea 100644
--- a/cwltool/schemas/draft-4/draft-4/echo-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/echo-tool.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 inputs:
   in:
     type: Any
diff --git a/cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl b/cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl
index f780c7319..a224a5c50 100644
--- a/cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl
+++ b/cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Test of capturing stderr output in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl b/cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl
index 9a70aa1d5..9a8c26aa1 100644
--- a/cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl
+++ b/cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Test of capturing stderr output in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl b/cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl
index 4bba74962..86ec03d05 100644
--- a/cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl
+++ b/cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Test of capturing stderr output in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/env-tool1.cwl b/cwltool/schemas/draft-4/draft-4/env-tool1.cwl
index 64f406392..af33b3b54 100644
--- a/cwltool/schemas/draft-4/draft-4/env-tool1.cwl
+++ b/cwltool/schemas/draft-4/draft-4/env-tool1.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 inputs:
   in: string
 outputs:
diff --git a/cwltool/schemas/draft-4/draft-4/env-tool2.cwl b/cwltool/schemas/draft-4/draft-4/env-tool2.cwl
index db5977a8e..8df0b64da 100644
--- a/cwltool/schemas/draft-4/draft-4/env-tool2.cwl
+++ b/cwltool/schemas/draft-4/draft-4/env-tool2.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 inputs:
   in: string
 outputs:
diff --git a/cwltool/schemas/draft-4/draft-4/env-wf1.cwl b/cwltool/schemas/draft-4/draft-4/env-wf1.cwl
index 11583218f..09268c5a1 100644
--- a/cwltool/schemas/draft-4/draft-4/env-wf1.cwl
+++ b/cwltool/schemas/draft-4/draft-4/env-wf1.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     in: string
diff --git a/cwltool/schemas/draft-4/draft-4/env-wf2.cwl b/cwltool/schemas/draft-4/draft-4/env-wf2.cwl
index fd5b321e7..9de645356 100644
--- a/cwltool/schemas/draft-4/draft-4/env-wf2.cwl
+++ b/cwltool/schemas/draft-4/draft-4/env-wf2.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
     in: string
diff --git a/cwltool/schemas/draft-4/draft-4/formattest-job.json b/cwltool/schemas/draft-4/draft-4/formattest-job.json
index da49d0103..0ff024096 100644
--- a/cwltool/schemas/draft-4/draft-4/formattest-job.json
+++ b/cwltool/schemas/draft-4/draft-4/formattest-job.json
@@ -1,7 +1,7 @@
 {
     "input": {
         "class": "File",
-        "path": "whale.txt",
+        "location": "whale.txt",
         "format": "edam:format_2330"
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/formattest.cwl b/cwltool/schemas/draft-4/draft-4/formattest.cwl
index 80dff90e4..d97e9be4d 100644
--- a/cwltool/schemas/draft-4/draft-4/formattest.cwl
+++ b/cwltool/schemas/draft-4/draft-4/formattest.cwl
@@ -1,6 +1,6 @@
 $namespaces:
   edam: "http://edamontology.org/"
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: CommandLineTool
 description: "Reverse each line using the `rev` command"
 inputs:
diff --git a/cwltool/schemas/draft-4/draft-4/formattest2-job.json b/cwltool/schemas/draft-4/draft-4/formattest2-job.json
index c70f7fb49..f706f6ed1 100644
--- a/cwltool/schemas/draft-4/draft-4/formattest2-job.json
+++ b/cwltool/schemas/draft-4/draft-4/formattest2-job.json
@@ -1,7 +1,7 @@
 {
     "input": {
         "class": "File",
-        "path": "ref.fasta",
+        "location": "ref.fasta",
         "format": "edam:format_1929"
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/formattest2.cwl b/cwltool/schemas/draft-4/draft-4/formattest2.cwl
index 377198de8..7ed3f9daa 100644
--- a/cwltool/schemas/draft-4/draft-4/formattest2.cwl
+++ b/cwltool/schemas/draft-4/draft-4/formattest2.cwl
@@ -3,7 +3,7 @@ $namespaces:
 $schemas:
   - EDAM.owl
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Reverse each line using the `rev` command"
 
 inputs:
diff --git a/cwltool/schemas/draft-4/draft-4/formattest3.cwl b/cwltool/schemas/draft-4/draft-4/formattest3.cwl
index fa4237699..e6342dfb4 100644
--- a/cwltool/schemas/draft-4/draft-4/formattest3.cwl
+++ b/cwltool/schemas/draft-4/draft-4/formattest3.cwl
@@ -5,7 +5,7 @@ $schemas:
   - EDAM.owl
   - gx_edam.ttl
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Reverse each line using the `rev` command"
 
 inputs:
diff --git a/cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl b/cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl
index 984142779..6144a785c 100644
--- a/cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl
+++ b/cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   ids:
diff --git a/cwltool/schemas/draft-4/draft-4/metadata.cwl b/cwltool/schemas/draft-4/draft-4/metadata.cwl
index b49e3f447..71c55e61a 100644
--- a/cwltool/schemas/draft-4/draft-4/metadata.cwl
+++ b/cwltool/schemas/draft-4/draft-4/metadata.cwl
@@ -6,7 +6,7 @@ $schemas:
   - foaf.rdf
   - dcterms.rdf
 
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 
diff --git a/cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl b/cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl
index 3460452f4..d953be546 100644
--- a/cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl
@@ -3,7 +3,7 @@
 class: ExpressionTool
 requirements:
   - class: InlineJavascriptRequirement
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   i1:
diff --git a/cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl b/cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl
index 129e26968..8cfb02dc8 100644
--- a/cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl
@@ -3,7 +3,7 @@
 class: ExpressionTool
 requirements:
   - class: InlineJavascriptRequirement
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   i1: Any
diff --git a/cwltool/schemas/draft-4/draft-4/optional-output.cwl b/cwltool/schemas/draft-4/draft-4/optional-output.cwl
index 46be1cdfe..ea058d3e9 100644
--- a/cwltool/schemas/draft-4/draft-4/optional-output.cwl
+++ b/cwltool/schemas/draft-4/draft-4/optional-output.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: "cwl:draft-4.dev2"
+cwlVersion: "cwl:draft-4.dev3"
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
diff --git a/cwltool/schemas/draft-4/draft-4/params.cwl b/cwltool/schemas/draft-4/draft-4/params.cwl
index 774023f48..6fd43a50f 100644
--- a/cwltool/schemas/draft-4/draft-4/params.cwl
+++ b/cwltool/schemas/draft-4/draft-4/params.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 inputs:
   bar:
     type: Any
diff --git a/cwltool/schemas/draft-4/draft-4/params2.cwl b/cwltool/schemas/draft-4/draft-4/params2.cwl
index 9993cef36..01967fcb3 100644
--- a/cwltool/schemas/draft-4/draft-4/params2.cwl
+++ b/cwltool/schemas/draft-4/draft-4/params2.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: InlineJavascriptRequirement
 
diff --git a/cwltool/schemas/draft-4/draft-4/parseInt-job.json b/cwltool/schemas/draft-4/draft-4/parseInt-job.json
index db0c8f496..b584ea23b 100644
--- a/cwltool/schemas/draft-4/draft-4/parseInt-job.json
+++ b/cwltool/schemas/draft-4/draft-4/parseInt-job.json
@@ -1,6 +1,6 @@
 {
     "file1": {
         "class": "File",
-        "path": "number.txt"
+        "location": "number.txt"
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl b/cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl
index bf1cc5a2d..5c3a77557 100755
--- a/cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl
@@ -3,7 +3,7 @@
 class: ExpressionTool
 requirements:
   - class: InlineJavascriptRequirement
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   file1:
diff --git a/cwltool/schemas/draft-4/draft-4/record-output-job.json b/cwltool/schemas/draft-4/draft-4/record-output-job.json
index 44d008189..df29550c2 100644
--- a/cwltool/schemas/draft-4/draft-4/record-output-job.json
+++ b/cwltool/schemas/draft-4/draft-4/record-output-job.json
@@ -1,6 +1,6 @@
 {
   "irec": {
-    "ifoo": {"path": "whale.txt", "class": "File"},
-    "ibar": {"path": "ref.fasta", "class": "File"}
+    "ifoo": {"location": "whale.txt", "class": "File"},
+    "ibar": {"location": "ref.fasta", "class": "File"}
   }
 }
\ No newline at end of file
diff --git a/cwltool/schemas/draft-4/draft-4/record-output.cwl b/cwltool/schemas/draft-4/draft-4/record-output.cwl
index b85251464..2e718da98 100644
--- a/cwltool/schemas/draft-4/draft-4/record-output.cwl
+++ b/cwltool/schemas/draft-4/draft-4/record-output.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: ShellCommandRequirement
 inputs:
diff --git a/cwltool/schemas/draft-4/draft-4/rename-job.json b/cwltool/schemas/draft-4/draft-4/rename-job.json
index 917bc989d..c8ff96069 100644
--- a/cwltool/schemas/draft-4/draft-4/rename-job.json
+++ b/cwltool/schemas/draft-4/draft-4/rename-job.json
@@ -1,6 +1,6 @@
 {
     "srcfile": {
-        "path": "whale.txt",
+        "location": "whale.txt",
         "class": "File"
     },
     "newname": "fish.txt"
diff --git a/cwltool/schemas/draft-4/draft-4/rename.cwl b/cwltool/schemas/draft-4/draft-4/rename.cwl
index 7b9de2931..e97743ee0 100644
--- a/cwltool/schemas/draft-4/draft-4/rename.cwl
+++ b/cwltool/schemas/draft-4/draft-4/rename.cwl
@@ -1,11 +1,11 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 baseCommand: "true"
 requirements:
-  CreateFileRequirement:
-    fileDef:
-      - filename: $(inputs.newname)
-        fileContent: $(inputs.srcfile)
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: $(inputs.newname)
+        entry: $(inputs.srcfile)
 inputs:
   srcfile: File
   newname: string
diff --git a/cwltool/schemas/draft-4/draft-4/revsort-job.json b/cwltool/schemas/draft-4/draft-4/revsort-job.json
index 3c6d0f889..f5671aab2 100644
--- a/cwltool/schemas/draft-4/draft-4/revsort-job.json
+++ b/cwltool/schemas/draft-4/draft-4/revsort-job.json
@@ -1,6 +1,6 @@
 {
   "input": {
     "class": "File",
-    "path": "whale.txt"
+    "location": "whale.txt"
   }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/revsort.cwl b/cwltool/schemas/draft-4/draft-4/revsort.cwl
index 8ca76ee08..e94b30ada 100644
--- a/cwltool/schemas/draft-4/draft-4/revsort.cwl
+++ b/cwltool/schemas/draft-4/draft-4/revsort.cwl
@@ -3,7 +3,7 @@
 #
 class: Workflow
 description: "Reverse the lines in a document, then sort those lines."
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 # Requirements & hints specify prerequisites and extensions to the workflow.
 # In this example, DockerRequirement specifies a default Docker container
diff --git a/cwltool/schemas/draft-4/draft-4/revtool.cwl b/cwltool/schemas/draft-4/draft-4/revtool.cwl
index 2a276f57d..ba3033c09 100644
--- a/cwltool/schemas/draft-4/draft-4/revtool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/revtool.cwl
@@ -2,7 +2,7 @@
 # Simplest example command line program wrapper for the Unix tool "rev".
 #
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Reverse each line using the `rev` command"
 
 # The "inputs" array defines the structure of the input object that describes
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl
index ab36fb4fa..0256066b3 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: Workflow
 inputs:
   inp:
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl
index f59ed9618..1894abee6 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: Workflow
 
 inputs:
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl
index 0e9192d2f..a691acf5d 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 $graph:
 
 - id: echo
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl
index aaf763da4..9cae1a2b2 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 $graph:
 - id: echo
   class: CommandLineTool
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl b/cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl
index eec267915..a8ffc6531 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: Workflow
 inputs:
   inp: string[]
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl b/cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl
index adb798a5c..abc20be26 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: Workflow
 
 inputs:
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl b/cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl
index 7cfe1250c..ce32fbd69 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 $graph:
 
 - id: echo
diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl b/cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl
index 8ff37bc53..c01d5650d 100644
--- a/cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl
+++ b/cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 $graph:
 - id: echo
   class: CommandLineTool
diff --git a/cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl b/cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl
index 33e6f20f3..0d8447442 100644
--- a/cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - $import: schemadef-type.yml
   - class: InlineJavascriptRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl b/cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl
index 15b873e80..4667f7894 100644
--- a/cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: Workflow
 
 requirements:
diff --git a/cwltool/schemas/draft-4/draft-4/search-job.json b/cwltool/schemas/draft-4/draft-4/search-job.json
index 0a6735da8..b5a1b61e5 100644
--- a/cwltool/schemas/draft-4/draft-4/search-job.json
+++ b/cwltool/schemas/draft-4/draft-4/search-job.json
@@ -1,7 +1,7 @@
 {
     "infile": {
         "class": "File",
-        "path": "whale.txt"
+        "location": "whale.txt"
     },
     "term": "find"
 }
diff --git a/cwltool/schemas/draft-4/draft-4/search.cwl b/cwltool/schemas/draft-4/draft-4/search.cwl
index 104a26437..dc32c0955 100644
--- a/cwltool/schemas/draft-4/draft-4/search.cwl
+++ b/cwltool/schemas/draft-4/draft-4/search.cwl
@@ -1,4 +1,4 @@
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 $graph:
 - id: index
   class: CommandLineTool
@@ -7,10 +7,9 @@ $graph:
     - valueFrom: input.txt
       position: 1
   requirements:
-    - class: CreateFileRequirement
-      fileDef:
-        - filename: input.txt
-          fileContent: $(inputs.file)
+    - class: InitialWorkDirRequirement
+      listing:
+        input.txt: $(inputs.file)
     - class: InlineJavascriptRequirement
 
   inputs:
@@ -19,7 +18,7 @@ $graph:
       type: File
       default:
         class: File
-        path: index.py
+        location: index.py
       inputBinding:
         position: 0
   outputs:
@@ -30,9 +29,9 @@ $graph:
       secondaryFiles:
         - ".idx1"
         - "^.idx2"
-        - '$(self.path+".idx3")'
-        - '$({"path": self.path+".idx4", "class": "File"})'
-        - '${ return self.path+".idx5"; }'
+        - '$(self.location+".idx3")'
+        - '$({"location": self.location+".idx4", "class": "File"})'
+        - '${ return self.location+".idx5"; }'
 
 - id: search
   class: CommandLineTool
@@ -47,14 +46,14 @@ $graph:
       secondaryFiles:
         - ".idx1"
         - "^.idx2"
-        - '$(self.path+".idx3")'
-        - '$({"path": self.path+".idx4", "class": "File"})'
-        - '${ return self.path+".idx5"; }'
+        - '$(self.location+".idx3")'
+        - '$({"location": self.location+".idx4", "class": "File"})'
+        - '${ return self.location+".idx5"; }'
     search.py:
       type: File
       default:
         class: File
-        path: search.py
+        location: search.py
       inputBinding:
         position: 0
     term:
diff --git a/cwltool/schemas/draft-4/draft-4/shelltest.cwl b/cwltool/schemas/draft-4/draft-4/shelltest.cwl
index 0ae27a3cb..9ccb34d52 100644
--- a/cwltool/schemas/draft-4/draft-4/shelltest.cwl
+++ b/cwltool/schemas/draft-4/draft-4/shelltest.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 description: "Reverse each line using the `rev` command then sort."
 requirements:
   - class: ShellCommandRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/sorttool.cwl b/cwltool/schemas/draft-4/draft-4/sorttool.cwl
index 447a502d2..7aeeadc03 100644
--- a/cwltool/schemas/draft-4/draft-4/sorttool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/sorttool.cwl
@@ -2,7 +2,7 @@
 # demonstrating command line flags.
 class: CommandLineTool
 description: "Sort lines using the `sort` command"
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 # This example is similar to the previous one, with an additional input
 # parameter called "reverse".  It is a boolean parameter, which is
diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl b/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl
index ba8418131..75b251d02 100644
--- a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: StepInputExpressionRequirement
 
diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.json b/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.json
index 8d6a9a6f1..b13324174 100644
--- a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.json
+++ b/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.json
@@ -2,7 +2,7 @@
     "in": {
         "file1": {
             "class": "File",
-            "path": "whale.txt"
+            "location": "whale.txt"
         }
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl b/cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl
index c5c9b8160..8d085aa37 100644
--- a/cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: StepInputExpressionRequirement
   - class: InlineJavascriptRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl b/cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl
index bd1acc8a8..54f70ba85 100644
--- a/cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl
+++ b/cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: StepInputExpressionRequirement
   - class: InlineJavascriptRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/template-tool.cwl b/cwltool/schemas/draft-4/draft-4/template-tool.cwl
index 7e3521382..f7a00024f 100755
--- a/cwltool/schemas/draft-4/draft-4/template-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/template-tool.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 class: CommandLineTool
 requirements:
   - class: DockerRequirement
@@ -8,10 +8,9 @@ requirements:
     expressionLib:
       - { $include: underscore.js }
       - "var t = function(s) { return _.template(s)({'inputs': inputs}); };"
-  - class: CreateFileRequirement
-    fileDef:
-      - filename: foo.txt
-        fileContent: >
+  - class: InitialWorkDirRequirement
+    listing:
+      foo.txt: >
           $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n"))
 inputs:
   - id: file1
diff --git a/cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl b/cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl
index 5ce6331be..884054d74 100644
--- a/cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl
+++ b/cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/testdir/a b/cwltool/schemas/draft-4/draft-4/testdir/a
new file mode 100644
index 000000000..e69de29bb
diff --git a/cwltool/schemas/draft-4/draft-4/testdir/b b/cwltool/schemas/draft-4/draft-4/testdir/b
new file mode 100644
index 000000000..e69de29bb
diff --git a/cwltool/schemas/draft-4/draft-4/testdir/c/d b/cwltool/schemas/draft-4/draft-4/testdir/c/d
new file mode 100644
index 000000000..e69de29bb
diff --git a/cwltool/schemas/draft-4/draft-4/tmap-job.json b/cwltool/schemas/draft-4/draft-4/tmap-job.json
index b4fec8a09..24cdda68a 100644
--- a/cwltool/schemas/draft-4/draft-4/tmap-job.json
+++ b/cwltool/schemas/draft-4/draft-4/tmap-job.json
@@ -1,7 +1,7 @@
 {
     "reads": {
         "class": "File",
-        "path": "reads.fastq"
+        "location": "reads.fastq"
     },
     "stages": [
         {
diff --git a/cwltool/schemas/draft-4/draft-4/tmap-tool.cwl b/cwltool/schemas/draft-4/draft-4/tmap-tool.cwl
index 8f8aca16a..1b6273e26 100755
--- a/cwltool/schemas/draft-4/draft-4/tmap-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/tmap-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 {
-    "cwlVersion": "cwl:draft-4.dev2",
+    "cwlVersion": "cwl:draft-4.dev3",
 
     "class": "CommandLineTool",
 
@@ -24,7 +24,7 @@
         type: File,
         default: {
           class: File,
-          path: args.py
+          location: args.py
         },
         inputBinding: {
           position: -1
diff --git a/cwltool/schemas/draft-4/draft-4/wc-job.json b/cwltool/schemas/draft-4/draft-4/wc-job.json
index 32ffc842b..598568d38 100644
--- a/cwltool/schemas/draft-4/draft-4/wc-job.json
+++ b/cwltool/schemas/draft-4/draft-4/wc-job.json
@@ -1,6 +1,6 @@
 {
     "file1": {
         "class": "File",
-        "path": "whale.txt"
+        "location": "whale.txt"
     }
 }
diff --git a/cwltool/schemas/draft-4/draft-4/wc-tool.cwl b/cwltool/schemas/draft-4/draft-4/wc-tool.cwl
index f129aaf0d..08ef2e77b 100755
--- a/cwltool/schemas/draft-4/draft-4/wc-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/wc-tool.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 inputs:
   file1: File
diff --git a/cwltool/schemas/draft-4/draft-4/wc2-tool.cwl b/cwltool/schemas/draft-4/draft-4/wc2-tool.cwl
index 4e5704e7d..510a6dc5c 100755
--- a/cwltool/schemas/draft-4/draft-4/wc2-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/wc2-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: InlineJavascriptRequirement
 
diff --git a/cwltool/schemas/draft-4/draft-4/wc3-tool.cwl b/cwltool/schemas/draft-4/draft-4/wc3-tool.cwl
index f7fff7e5a..6aa6986f4 100644
--- a/cwltool/schemas/draft-4/draft-4/wc3-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/wc3-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 
 requirements:
   - class: InlineJavascriptRequirement
diff --git a/cwltool/schemas/draft-4/draft-4/wc4-tool.cwl b/cwltool/schemas/draft-4/draft-4/wc4-tool.cwl
index 4a4404579..21e08a530 100644
--- a/cwltool/schemas/draft-4/draft-4/wc4-tool.cwl
+++ b/cwltool/schemas/draft-4/draft-4/wc4-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev2
+cwlVersion: cwl:draft-4.dev3
 requirements:
   - class: InlineJavascriptRequirement
 
diff --git a/cwltool/stdfsaccess.py b/cwltool/stdfsaccess.py
index 618d35ac0..cfdcb657b 100644
--- a/cwltool/stdfsaccess.py
+++ b/cwltool/stdfsaccess.py
@@ -13,10 +13,19 @@ def _abs(self, p):  # type: (unicode) -> unicode
         return abspath(p, self.basedir)
 
     def glob(self, pattern):  # type: (unicode) -> List[unicode]
-        return glob.glob(self._abs(pattern))
+        return ["file://%s" % self._abs(l) for l in glob.glob(self._abs(pattern))]
 
     def open(self, fn, mode):  # type: (unicode, str) -> BinaryIO
         return open(self._abs(fn), mode)
 
     def exists(self, fn):  # type: (unicode) -> bool
         return os.path.exists(self._abs(fn))
+
+    def isfile(self, fn):
+        return os.path.isfile(self._abs(fn))
+
+    def isdir(self, fn):
+        return os.path.isdir(self._abs(fn))
+
+    def listdir(self, fn):
+        return [abspath(l, fn) for l in os.listdir(self._abs(fn))]
diff --git a/cwltool/update.py b/cwltool/update.py
index 19a70a56b..dfe76b14e 100644
--- a/cwltool/update.py
+++ b/cwltool/update.py
@@ -324,11 +324,27 @@ def _draft3toDraft4dev1(doc, loader, baseuri):
     # type: (Any, Loader, str) -> Any
     if isinstance(doc, dict):
         if "class" in doc and doc["class"] == "Workflow":
+            def fixup(f):
+                doc, frg = urlparse.urldefrag(f)
+                frg = '/'.join(frg.rsplit('.', 1))
+                return doc + "#" + frg
+
             for step in doc["steps"]:
                 step["in"] = step["inputs"]
                 step["out"] = step["outputs"]
                 del step["inputs"]
                 del step["outputs"]
+                for io in ("in", "out"):
+                    for i in step[io]:
+                        i["id"] = fixup(i["id"])
+                        if "source" in i:
+                            i["source"] = [fixup(s) for s in aslist(i["source"])]
+                            if len(i["source"]) == 1:
+                                i["source"] = i["source"][0]
+                if "scatter" in step:
+                    step["scatter"] = [fixup(s) for s in aslist(step["scatter"])]
+            for out in doc["outputs"]:
+                out["source"] = fixup(out["source"])
         for key, value in doc.items():
             doc[key] = _draft3toDraft4dev1(value, loader, baseuri)
     elif isinstance(doc, list):
@@ -360,6 +376,39 @@ def draft4Dev1toDev2(doc, loader, baseuri):
     """Public updater for draft-4.dev1 to draft-4.dev2."""
     return (_draft4Dev1toDev2(doc, loader, baseuri), "draft-4.dev2")
 
+
+def _draft4Dev2toDev3(doc, loader, baseuri):
+    # type: (Any, Loader, str) -> Any
+    if isinstance(doc, dict):
+        if "class" in doc and doc["class"] == "File":
+            doc["location"] = doc["path"]
+            del doc["path"]
+        if "secondaryFiles" in doc:
+            for i, sf in enumerate(doc["secondaryFiles"]):
+                if "$(" in sf or "${" in sf:
+                    doc["secondaryFiles"][i] = sf.replace('"path"', '"location"').replace(".path", ".location")
+
+        if "class" in doc and doc["class"] == "CreateFileRequirement":
+            doc["class"] = "InitialWorkDirRequirement"
+            doc["listing"] = []
+            for f in doc["fileDef"]:
+                doc["listing"].append({
+                    "entryname": f["filename"],
+                    "entry": f["fileContent"]
+                })
+            del doc["fileDef"]
+        for key, value in doc.items():
+            doc[key] = _draft4Dev2toDev3(value, loader, baseuri)
+    elif isinstance(doc, list):
+        doc = [_draft4Dev2toDev3(item, loader, baseuri) for item in doc]
+
+    return doc
+
+def draft4Dev2toDev3(doc, loader, baseuri):
+    # type: (Any, Loader, str) -> Tuple[Any, str]
+    """Public updater for draft-4.dev2 to draft-4.dev3."""
+    return (_draft4Dev2toDev3(doc, loader, baseuri), "draft-4.dev3")
+
 UPDATES = {
     "draft-2": draft2toDraft3dev1,
     "draft-3": draft3toDraft4dev1
@@ -372,13 +421,14 @@ def draft4Dev1toDev2(doc, loader, baseuri):
     "draft-3.dev4": draftDraft3dev4toDev5,
     "draft-3.dev5": draftDraft3dev5toFinal,
     "draft-4.dev1": draft4Dev1toDev2,
-    "draft-4.dev2": None
+    "draft-4.dev2": draft4Dev2toDev3,
+    "draft-4.dev3": None
 } # type: Dict[unicode, Callable[[Any, Loader, str], Tuple[Any, str]]]
 
 ALLUPDATES = UPDATES.copy()
 ALLUPDATES.update(DEVUPDATES)
 
-LATEST = "draft-4.dev2"
+LATEST = "draft-4.dev3"
 
 def identity(doc, loader, baseuri):  # pylint: disable=unused-argument
     # type: (Any, Loader, str) -> Tuple[Any, Union[str, unicode]]
diff --git a/cwltool/workflow.py b/cwltool/workflow.py
index 48c0069da..e793d901a 100644
--- a/cwltool/workflow.py
+++ b/cwltool/workflow.py
@@ -298,7 +298,7 @@ def valueFromFunc(k, v):  # type: (Any, Any) -> Any
     def run(self, **kwargs):
         _logger.debug(u"[%s] workflow starting", self.name)
 
-    def job(self, joborder, output_callback, move_outputs=True, **kwargs):
+    def job(self, joborder, output_callback, **kwargs):
         # type: (Dict[unicode, Any], Callable[[Any, Any], Any], bool, **Any) -> Generator[WorkflowJob, None, None]
         self.state = {}
         self.processStatus = "success"
@@ -319,8 +319,6 @@ def job(self, joborder, output_callback, move_outputs=True, **kwargs):
             for out in s.tool["outputs"]:
                 self.state[out["id"]] = None
 
-        output_dirs = set()
-
         completed = 0
         while completed < len(self.steps) and self.processStatus == "success":
             made_progress = False
@@ -333,8 +331,6 @@ def job(self, joborder, output_callback, move_outputs=True, **kwargs):
                     for newjob in step.iterable:
                         if newjob:
                             made_progress = True
-                            if newjob.outdir:
-                                output_dirs.add(newjob.outdir)
                             yield newjob
                         else:
                             break
@@ -351,43 +347,6 @@ def job(self, joborder, output_callback, move_outputs=True, **kwargs):
         if wo is None:
             raise WorkflowException("Output for workflow not available")
 
-        if move_outputs:
-            targets = set()  # type: Set[str]
-            conflicts = set()
-
-            outfiles = findfiles(wo)
-
-            for f in outfiles:
-                for a in output_dirs:
-                    if f["path"].startswith(a):
-                        src = f["path"]
-                        dst = os.path.join(self.outdir, src[len(a)+1:])
-                        if dst in targets:
-                            conflicts.add(dst)
-                        else:
-                            targets.add(dst)
-
-            for f in outfiles:
-                for a in output_dirs:
-                    if f["path"].startswith(a):
-                        src = f["path"]
-                        dst = os.path.join(self.outdir, src[len(a)+1:])
-                        if dst in conflicts:
-                            sp = os.path.splitext(dst)
-                            dst = u"%s-%s%s" % (sp[0], str(random.randint(1, 1000000000)), sp[1])
-                        dirname = os.path.dirname(dst)
-                        if not os.path.exists(dirname):
-                            os.makedirs(dirname)
-                        _logger.debug(u"[%s] Moving '%s' to '%s'", self.name, src, dst)
-                        shutil.move(src, dst)
-                        f["path"] = dst
-
-            for a in output_dirs:
-                if os.path.exists(a) and empty_subtree(a):
-                    if kwargs.get("rm_tmpdir", True):
-                        _logger.debug(u"[%s] Removing intermediate output directory %s", self.name, a)
-                        shutil.rmtree(a, True)
-
         _logger.info(u"[%s] outdir is %s", self.name, self.outdir)
 
         output_callback(wo, self.processStatus)
diff --git a/tests/echo.cwl b/tests/echo.cwl
index 6eb6a23a6..da6943328 100644
--- a/tests/echo.cwl
+++ b/tests/echo.cwl
@@ -1,4 +1,4 @@
-cwlVersion: cwl:draft-3
+cwlVersion: cwl:draft-4.dev2
 class: CommandLineTool
 inputs:
   - id: inp
diff --git a/tests/test_pathmapper.py b/tests/test_pathmapper.py
index 7e4af9e5b..b54c89a3f 100644
--- a/tests/test_pathmapper.py
+++ b/tests/test_pathmapper.py
@@ -9,13 +9,12 @@
 class TestPathMapper(unittest.TestCase):
 
     def test_subclass(self):
-        
+
         class SubPathMapper(PathMapper):
 
-            def __init__(self, referenced_files, basedir, new):
-                super(SubPathMapper, self).__init__(referenced_files, basedir)
+            def __init__(self, referenced_files, basedir, stagedir, new):
+                super(SubPathMapper, self).__init__(referenced_files, basedir, stagedir)
                 self.new = new
 
-        a = SubPathMapper([], '', "new")
+        a = SubPathMapper([], '', '', "new")
         self.assertTrue(a.new, "new")
-        
diff --git a/tests/test_toolargparse.py b/tests/test_toolargparse.py
index 6c3e05680..dfa108318 100644
--- a/tests/test_toolargparse.py
+++ b/tests/test_toolargparse.py
@@ -8,7 +8,7 @@ class ToolArgparse(unittest.TestCase):
 
     script='''
 #!/usr/bin/env cwl-runner
-cwlVersion: "draft-3"
+cwlVersion: "draft-4.dev2"
 class: CommandLineTool
 description: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"
 inputs:
@@ -28,7 +28,7 @@ class ToolArgparse(unittest.TestCase):
 
     script2='''
 #!/usr/bin/env cwl-runner
-cwlVersion: 'cwl:draft-3'
+cwlVersion: 'cwl:draft-4.dev2'
 class: CommandLineTool
 inputs:
   - id: bdg