In case we have a git clone from Linux that is accessed via cygwin git
the files executable status will be derived from the file content (shebang)
and won't match the git repo, leading to a initially dirty tree.
This can be worked around by setting "core.filemode=false", but let's try
to match the cygwin permissions with the in-repo permissions so this isn't
needed.
In some cases this will introduce cycles which could likely be cleaned
up by only depending on some unix tools instead of the whole autotools.
Rebuilding doesn't make much sense at this point since it just adds a subset
of base-devel which is still installed by default.
Christoph Reiter