> 2. Kill EGIT_HAS_SUBMODULES and autodetect submodules,

I'm disagreed. Sometimes submodules, that repo suggests is unneded,
since they fetches external package, that specified as RDEP.

> 
> 3. Kill EGIT_OPTIONS since it limits the possibility of changing eclass
>    code,

:-/

> 4. Kill EGIT_MASTER (it's more trouble than benefit),

Only if EGIT_BRANCH will stay on it's place.

> 5. Possibly kill EGIT_PROJECT -- it won't be good enough anymore,

Why?

> 6. Kill EGIT_NONBARE and support bare checkouts only. Supporting two
>    different layouts introduces a lot redundant code.

AFAIR, that was issues (including shallow clones and so on), that
refuses to use bare repo.

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