Use wstool but keep git directories organized under a custom structure

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I'm not sure I understand you correctly, but the .rosinstall format supports specifying a destination for clones/checkouts of repositories with the local-name property.

The documentation on the file format describes it as:

Inside every top level dictionary there is one required key, local-name this represents the path where to install files. It will support both workspace relative paths as well as absolute paths.

So if you want to keep things in a different directory than directly in your source space, you could do that by setting local-name to something like:

some_dir/other_dir/baxter/..

Each entry has its own local-name key, so each repository can be placed in a different directory.