Make git_index_read_tree preserve stat cache where possible

Instead of just blowing away the stat cache data when loading a
new tree into the index, this checks if each loaded item has a
corresponding existing item with the same OID and if so, copies
the stat data from the old item to the new one so it will not be
blown away.

improve test for index extension truncation

Added support for setting transport flags (No check SSL cert) to git_clo...

Introduce git_reference_shorthand

remote: make default tag retrieving behaviour consistent

Build with the system's http-parser installation if available

Default for newly created remotes will be auto.
Default when loading existing remotes with no tag retrieving behaviour set, was already auto.

thread: fix segfault on Windows 64 bits

`lpExitCode` is a pointer to a long. A long is 32 bits wide on Windows.

It means that on Windows 64bits, `GetExitCodeThread()` doesn't set/clear the high-order bytes of the 64 bits memory space pointed at by `value_ptr`.

allow (ignore) bare slash in gitignore

Fix memory leak in oid shortener tests

Fix two typos in the merge docs.

packbuilder: also write index in git_packbuilder_write

git_packbuilder_write() used to write a packfile to the passed file
path. Instead, ask for a destination directory and create both the
packfile and an index, as most users probably do expect.

tests: don't verify SSH unsupported with GIT_SSH

Fix documentation of git_branch_delete.

The reference should be freed by the user, not the library.

qsort_r appeared in glibc 2.8

Various cleanups and tweaks

This adds ~/ prefix expansion for the value of core.attributesfile
and core.excludesfile, plus it fixes the fact that the attributes
cache was holding on to the string data from the config for a long
time (instead of making its own strdup) which could have caused a
problem if the config was refreshed.  Adds a test for the new
expansion capability.

This improves the docs for GIT_DIFF_INCLUDE_UNTRACKED_CONTENT as
well as the other flags related to UNTRACKED items in diff, plus
it makes that flag now automatically turn on
GIT_DIFF_INCLUDE_UNTRACKED which seems like a reasonable dwim type
of change.

The GIT_CONFIG_LEVEL constants actually work well as an enum
because they are mutually exclusive, so this adds a typedef to
the enum and uses that everywhere that one of these constants are
expected, instead of the old code that typically used an unsigned
int.

This adds docs for the cache control options to git_libgit2_opts
and also tweaks the cache code so that if the cache is disabled,
then the next time we attempt to insert something into the cache
in question, we will actually clear any old cached objects.

Apparently this makes things easier to bind in some languages.

qsort_r is broken on HURD, avoid

Cherry picking REUC fixes

In theory, if there was a problem reading the REUC data, the
read_reuc() routine could have left uninitialized and invalid
data in the git_index vector.  This moves the line that inserts a
new entry into the vector down to the bottom of the routine so we
know all the content is already valid.  Also, per @linquize, this
uses calloc to ensure no uninitialized data.

introduce git_conflict_iterator