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Like a recursive grep but it understands what's not part of the source tree and can be used on any commit, etc. rather than simply what you have checked out at the moment. It's quite useful simply for not looking in .git, build output, etc. without excluding that stuff.
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I think subtrees make more sense for tightly bound components and repo is a nicer approach than submodules for other things. Submodules are bad enough that both AOSP and Chromium invented their own versions of it to work around how broken/weird/painful they are to deal with.
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I don't mind repo because it's simply a text file describing repositories via branch, tag, revision, etc. and it's nice to deal with for overriding repositories and so on. It essentially works like submodules if you reference things via revision which you do for a release.
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The manifest is in a repository by itself with nothing else. If you want, you can refer to everything via specific revisions. Generally, you refer to stuff via tags or even branches for development and for a build you generate a frozen revision manifest with repo manifest -r.
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