The idea...sometimes, a filemode is user-specified via an
explicit git_index_entry.  In this case, believe the user, always.

Sometimes, it is instead built up by statting the file system.  In
those cases, go with the existing logic we have to determine
whether the file system supports all filemodes and symlinks, and
make the best guess.

On file systems which have full filemode and symlink support, this
commit should make no difference.  On others (most notably Windows),
this will fix problems things like:
* git_index_add and git_index_add_frombuffer() should be believed.
* As a consequence, git_checkout_tree should make the filemodes in
the index match the ones in the tree.
* And diffs with GIT_DIFF_UPDATE_INDEX don't write the wrong filemodes.
* And merges, and probably other downstream stuff now fixed, too.

This makes my previous changes to checkout.c unnecessary,
so they are now reverted.

Also, added a test for index_entry permissions from git_index_add
and git_index_add_frombuffer, both of which failed before these changes.

git_checkout_tree() has some fallback behaviors for file systems
which don't have full support of filemodes.  Generally works fine,
but if a given file had a change of type from a 0644 to 0755 (i.e.,
you add executable permissions), the fallback behavior incorrectly
triggers when writing hte updated index.

This would cause a git_checkout_tree() command, even with the
GIT_CHECKOUT_FORCE option set, to leave a dirty index on Windows.

Also added checks to an existing test to catch this case.

Entry argument passed to git_index_add_frombuffer() should be const

gitignore: ignore vim swapfiles

Clear temporary buffer when filtering

If we are using a temporary buffer for filtering, be sure to clear
it before using it, in case the file that we are filtering is empty.

squash some leaks

Add a custom param to git_smart_subtransport_definition

WinHTTP for MinGW

note: use a git_buf to return the default namespace

examples: add remote example.

checkout: report correct invalid path

In case of a bad url or other error during the connection setup, we
close the stream via free.

fix changelog

mkdir-ext: Assume directories don't exist; fix all race cases

win32 resource: allow custom comments field in DLL

Allow merges of files (and trees) with whitespace problems/fixes

The smart transport has already take the payload param. For the
sub transport a payload param is useful for the implementer.

clar: update to 08f434d

Update tips fixes

Lower case the include directive of windows header

PERF: In MERGE, lazily compute is_binary

Initialize refs vector in git_remote_update_tips().

Otherwise, bailing out early when ls_to_vector() fails accesses
uninitialized memory.

The caller has otherwise no way to know how long the string will be
allocated or ability to free it.

This fixes #2944.