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The rosws workspace does not get automatically "indexed" fully. Instead you can imagine that subfolders of the workspace are not "active", unless they get activated.
Only entries in the .rosinstall file are active, and being "indexed". The sandbox is only "indexed" if you have that in your .rosinstall file. rosws set adds a folder to your .rosinstall file, it does not mark the folder as a workspace, it marks the folder as being an active part of the workspace.
The indexing is using a cache file, so if you install or remove packages, the cache can be stale, and roscd and similar commands may not work correctly until the cache is refresehd. The
$ rospack profile
command refreshes the cache manually.
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