submodule: detect conflicts with existing gitdir configs

Credit goes to Emily and Josh for testing and noticing a corner-case
which caused conflicts with existing gitdir configs to silently pass
validation, then fail later in add_submodule() with a cryptic error:

fatal: A git directory for 'nested%2fsub' is found locally with remote(s):
  origin	/.../trash directory.t7425-submodule-gitdir-path-extension/sub

This change ensures the validation step checks existing gitdirs for
conflicts. We only have to do this for submodules having gitdirs,
because those without submodule.%s.gitdir need to be migrated and
will throw an error earlier in the submodule codepath.

Quoting Josh:
 My testing setup has been as follows:
 * Using our locally-built Git with our downstream patch of [1] included:
   * create a repo "sub"
   * create a repo "super"
   * In "super":
     * mkdir nested
     * git submodule add ../sub nested/sub
     * Verify that the submodule's gitdir is .git/modules/nested%2fsub
 * Using a build of git from upstream `next` plus this series:
   * git config set --global extensions.submodulepathconfig true
   * git clone --recurse-submodules super super2
   * create a repo "nested%2fsub"
   * In "super2":
     * git submodule add ../nested%2fsub

At this point I'd expect the collision detection / encoding to take
effect, but instead I get the error listed above.
End quote

Suggested-by: Josh Steadmon <steadmon@google.com>
Signed-off-by: Adrian Ratiu <adrian.ratiu@collabora.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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