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Looking at the release notes for espflash v3.0.0-rc1, it seems that the partition table can now be specified in the espflash.toml file. (As added in #551)
However, it seems that espflash will only look for this file in the current directory, or the user's main configuration directory (See these lines of code. It should support looking at parent directories so as to support cargo workspaces with multiple crates.
This is especially useful if cargo test is used, as that command will execute in the individual crates sub-directories in the workspace. With the current search method used by espflash, this would require creating an additional espflash.toml in each crate's directory, instead of a single espflash.toml in the workspace directory.