Why my below directory are shown as hidden inside my github repository
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This is not a directory, this is a submodule, see [this](https://git-scm.com/book/en/v2/Git-Tools-Submodules). – Elias Holzmann Jan 17 '16 at 08:49
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It seems as though this is because each of those folders are actually repositories in their own right.
In these cases, I believe git see's these folders as submodules and doesn't necessarily store changes made to those folders. Instead, it will let each folder manage it's own history and your main repository will only store pointers to those projects.
So in the context of your global project, those folders are "empty" because this repository does not monitor changes made to them.
If you'd rather manage those plugins yourself and "loose" the git repositories and history of those plugins, simply remove the .git folder from each of those folders - they won't manage their own version control and your main repository will take over to monitor their changes.
Lix
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Those are not submodules, but simply the record of git nested repo (only the gitlink, special entry in the index) is recorded.
See "Difference between nested git repos and submodules"
Check on your local repo: each of those folders is likely to include a .git/ subfolder.
