Fix win32 lstat

VS-Build: Append C_FLAGS to the end of the already given ones.

My other PR revealed, that the /W4 parameter, we give to MSVC is ignored
because cmake set CMAKE_C_FLAGS already to /W3 and we overwrite it.

The command line tools gave me a D9025 warning for this on every file and
looking into the project properties page on MSVC 2008 tells, that it has
the warning level set to /W3.

However, the warnings introduced by /W4 are far to useless for having
them enabled. So just disable them.

Don't use precompiled headers for command-line based VC builds.

The reason, why libgit2 currently cannot support compiling via the command-line
tools cl/nmake from WinSDK and/or Microsoft Visual Studio, seems to be a
missing dependency on the generated precompiled header file.

The Visual Studio IDE automatically inserts this dependency when it sees the
right combination of "/Y" parameters.

This patch allows to compile using command line tools by disabling precompiled
headers for NON-IDE builds.

Filename validation

This prevents the index api from calling write_tree() with a
bogus tree.

As per core git.

Indexer: Avoid a possible double-deletion in error case

Itsy bitsy tiny winy minor api related fixes

Passing 0 as the index now retrieves the most recent entry instead
of the oldest one.

odb: recursively load alternates

The maximum depth is 5, like in git

Win32 fixes for diff/checkout/reset

Add option to ignore file mode in diffs

Diff API signatures

A number of diff APIs and the `git_checkout_index` API take a
`git_repository` object an operate on the index.  This updates
them to take a `git_index` pointer explicitly and only fall back
on the `git_repository` index if the index input is NULL.  This
makes it easier to operate on a temporary index.

The index iterator could previously only be created from a repo
object, but this allows creating an iterator from a `git_index`
object instead (while keeping, though renaming, the old function).

The diff API is not in the parameter order one would expect from
other libgit2 APIs.  This fixes that.

The reset hard tests had hardcoded expected file content and was
not correctly compensating for CRLF filtering when a file needed
to be reverted by the reset hard.  This fixes that.