Restructure documentation sidebar

[NielsGeudens]

• restructured the user guide documentation to match the dropdown menus in the platform.
• created dedicated pages for investigations, studies and assays. Currently, these are focused on ISA-JSON compliant ISA, but could be expanded still. Content of the new pages was taken from 'Designing an ISA-JSON compliant experiment'. This page is no longer linked, but left intact if changes/reverts need to be done.
• Created dedicated pages for SOPs and publications. Content needs to be expanded still.

Overall, no content was removed or added, only the structure was changed.

[kdp-cloud]

@PhilReedData The git history is correct now.

[PhilReedData]

Thanks @kdp-cloud. I've run it locally, it looks much better, thank you. I have a few questions.

1. There is no longer a link to designing-experiments-isajson-compliant.md - is that deliberate? It is under Experiments but commented out.
2. We have an anchor link to a heading within a page, instead of a whole page, which I've been trying to remove. Under Experiments > Experiment Sample Templates > Browse samples by Experiment Sample Template (/help/user-guide/browsing#browsing-samples-by-experiment-sample-templates). These links do not work correctly with ETT, they will not scroll to the heading when clicked from menus (I have reported this before). Can we remove this link, or create a new page for it?
3. The page exporting-experiments-as-isajson.md now appears in three places in the Experiments menu, under Investigations, Studies and Assays. Could we instead have it appear once, below Assays at the same level?

[NielsGeudens]

Hi @PhilReedData ,
Thanks for looking at this.

1. yes, it is deliberate that the file is no longer linked. The content of this page is now more distributed under investigations.md, studies.md and assays.md. However, I left the file intact, as I did not want to delete it yet. However, since the content is now somewhere else, it is probably more of a mental reassurance, rather than something practical..
2. We can remove the link, though I think querying by EST deserves its own page. However, it should also feature under the general 'browsing' page. Perhaps we can provide a link to the dedicated page in the general 'browsing' page, or duplicate the content (I'd rather not though)
3. Yes, it can be placed under assays. However, this is one of the first things I would like to tackle content-wise, once the restructuring is done.

If you need me to make any changes, please let me know!

[PhilReedData]

Morning @kdp-cloud.

1. I'm happy to keep the unlinked file but could you please add a notice to the top to explain that this page is no longer maintained, please see X, Y, Z pages instead? Use the message box feature: {% include callout.html type="warning" content="..." %}
2. I just noticed, the anchor link was incorrect, it should be #browse-samples-by-experiment-sample-template, not #browsing-samples-by-experiment-sample-templates (first and last word are different) -- if you change it, does it work better now?
3. I've made a draft item in the new Project for this -- can you see the Project? I'm not sure yet what you're suggesting to tackle content-wise here. If it is going to remain as one page, I'd prefer to link to it once as I said on Friday, but if you want to make this into three different pages, let's keep it in the menu in three places.

I'm keen to use this new GitHub Project for planning documentation work. It's currently set to private, I will ask Stuart to change this if necessary. After we close this PR, we can move on to the relative URL PR, then perhaps you and I and Niels could plan the order of the next steps using this project and issues? Many thanks.

[NielsGeudens]

I deleted the file anyway. Sorry for the confusion.
I updated the anchor link.
I can see the project, and would be happy to contribute to this.