A package-specific documentation (README.md) should be placed inside the package.
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analyzers: a place/namespace to keep analyzers.
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external: external packages should be here. A good place for git submodules.
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githooks: a place for custom git hooks. They can be autolinked by the init.sh script.
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local: a place for local installations. Should be kept empty in a repo, but is used otherwise.
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script: shell (helper) scripts live here.
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util: a place to keep standalone utilities.
Start with script/setup/init.sh that will help to set up some basics.