Fix stash save bug with fast path index check

We've introduced a manifest for the clib version system that includes a
version number; we should update it at release time to correspond with
the version number in the header.

This PR introduces a new top-level file, `package.json`, which enables this repository compatibility with [`clib`](https://github.com/clibs/clib), an open source C package manager.  By doing this, users of `clib` can quickly include the `libgit2` library within their project.

path: unify `git_path_is_*` APIs

Fix negative gitignore rules with leading directories 

Custom memory allocators

Tie in the newly created infrastructure for swapping out memory
allocators into our settings code. A user can now simply use the new
option "GIT_OPT_SET_ALLOCATOR" with `git_libgit2_opts`, passing in an
already initialized allocator structure as vararg.

Currently, our memory allocators are being redirected to the correct
implementation at compile time by simply using macros. In order to make
them swappable at runtime, this commit reshuffles that by instead making
use of a global "git_allocator" structure, whose pointers are set up to
reference the allocator functions. Like this, it becomes easy to swap
out allocators by simply setting these function pointers.

In order to initialize a "git_allocator", our provided allocators
"stdalloc" and "crtdbg" both provide an init function. This is being
called to initialize a passed in allocator struct and set up its members
correctly.

No support is yet included to enable users of libgit2 to switch out the
memory allocator at a global level.

Our desired architecture would make allocators completely pluggable,
such that users of libgit2 can swap out memory allocators at runtime.
While making e.g. debugging easier by not having to do a separate build,
this feature can also help maintainers of bindings for libgit2 by tying
the memory allocations into the other language's memory system.

In order to do so, though, we first need to make our two different
pre-existing allocators "stdalloc" and "crtdbg" have the same function
signatures, as the "crtdbg" allocators all have an additional file and
line argument. This is required to build correct stack traces for
debugging memory allocations. As that feature may also be interesting to
authors of other applications for debugging libgit2, we now simply add
these arguments to our standard allocators.

Obviously, this may come with a performance penalty. During some simple
benchmarks no real impact could be measured though in contrast to a
simple pluggable allocator. The following table summarizes the
benchmarks. There were three different builds with our current standard
allocator ("standard"), with pluggable authenticators accessed via
function pointers ("pluggable") and for pluggable authenticators with
file and line being added ("fileline"). Furthermore, there were three
scenarios for 100.000.000 allocations of 100B ("small alloc"),
100.000.000 allocations of 100KB ("medium alloc"), and 1.000.000
allocations of 100MB. All results are best of 10 runs.

|------------|-------------------|-------------------|-------------------|
| build/test | small alloc       | medium alloc      | big alloc         |
|------------|-------------------|-------------------|-------------------|
| standard   | 4539779566, +0.0% | 5912927186, +0.0% | 5166935308, +0.0% |
|------------|-------------------|-------------------|-------------------|
| pluggable  | 4611074505, +1.5% | 5979185308, +1.1% | 5388776352, +4.2% |
|------------|-------------------|-------------------|-------------------|
| fileline   | 4588338192, +1.1% | 6004951910, +1.5% | 4942528135, -4.4% |
|------------|-------------------|-------------------|-------------------|

As can be seen, there is a performance overhead for pluggable
allocators. Furthermore, it can also be seen that there is some big
variance between runs, especially in the "big alloc" scenario. This is
probably being caused by nondeterministic behaviour in the kernel for
dynamic allocations. Still, it can be observed that there should be no
real difference between the "pluggable" and "fileline" allocators.

Our "util.h" header is a grabbag of various different functions, where
many don't have a clear group they belong to. Our set of allocator
functions though can be clearly singled out as a single group of
functions that always belongs together. Furthermore, we will need to
implement additional functions relating to our allocators subsystem when
moving to pluggable allocators. Thus, we should just move these
functions into their own "alloc" module.

Right now, the standard allocator is being declared as part of the
"util.h" header as a set of inline functions. As with the crtdbg
allocator functions, these inline functions make it hard to convert to
function pointers for our allocators.

Create a new "stdalloc" module containing our standard allocations
functions to split these out. Convert the existing allocators to macros
which make use of the stdalloc functions.

Currently, the `git__free` function is being defined in a single place,
only, disregarding whether we use our standard allocators or the crtdbg
allocators. This makes it a bit harder to convert our code base to use
pluggable allocators, and furthermore makes the border between our two
allocators a bit more blurry.

Implement a separate `git__crtdbg__free` function for the crtdbg
allocator in order to completely separate both allocator
implementations.

The crtdbg allocators are currently being implemented as inline
functions as part of the "w32_crtdbg_stacktrace.h" header. As we are
moving towards pluggable allocators with the help of function pointers,
though, we cannot make use of inlining anymore. Instead, we can only
have a single implementation of these allocating functions.

Move all implementations of the crtdbg allocators into
"w32_crtdbg_stacktrace.c".

index: Fix alignment issues in write_disk_entry()

travis: war on leaks

If the index contains stat data for a modified file, and the file is
not racily dirty, and there exists an untracked working tree directory
alphabetically after that file, and there are no other changes to the
repo, then git_stash_save would fail. It would confuse the untracked
working tree directory for the modified file, because they have the
same sha: zero.  The wt directory has a sha of zero because it's a
directory, and the file would have a zero sha because we wouldn't read
the file -- we would just know that it doesn't match the index.  To
fix this confusion, we simply check mode as well as SHA.

refdb_fs: fix regression: failure when globbing for non-existant references

tests: submodule: do not rely on config iteration order

The goal is to let cmake manage the parallelism

==17851== Invalid free() / delete / delete[] / realloc()
==17851==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==17851==    by 0x60BBE2B: __libc_freeres (in /lib/x86_64-linux-gnu/libc-2.19.so)
==17851==    by 0x4A256BC: _vgnU_freeres (in /usr/lib/valgrind/vgpreload_core-amd64-linux.so)
==17851==    by 0x5F8F16A: __run_exit_handlers (exit.c:97)
==17851==    by 0x5F8F1F4: exit (exit.c:104)
==17851==    by 0x5F74F4B: (below main) (libc-start.c:321)
==17851==  Address 0x63153c0 is 0 bytes inside data symbol "noai6ai_cached"

==2957== 912 bytes in 19 blocks are still reachable in loss record 323 of 369
==2957==    at 0x4C2AB80: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2957==    by 0x675B120: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x675BDF8: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x675FE0D: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x6761DC4: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x676477E: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x675B071: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x675B544: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x675914B: gcry_control (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==2957==    by 0x5D30EC9: libssh2_init (in /usr/lib/x86_64-linux-gnu/libssh2.so.1.0.1)
==2957==    by 0x66BCCD: git_transport_ssh_global_init (ssh.c:910)
==2957==    by 0x616443: init_common (global.c:65)

==18109== 664 bytes in 1 blocks are still reachable in loss record 279 of 339
==18109==    at 0x4C2AB80: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==18109==    by 0x675B120: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==18109==    by 0x675C13C: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==18109==    by 0x675C296: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==18109==    by 0x679BD14: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==18109==    by 0x679CC64: ??? (in /lib/x86_64-linux-gnu/libgcrypt.so.11.8.2)
==18109==    by 0x6A64946: ??? (in /usr/lib/x86_64-linux-gnu/libgnutls.so.26.22.6)
==18109==    by 0x6A116E8: ??? (in /usr/lib/x86_64-linux-gnu/libgnutls.so.26.22.6)
==18109==    by 0x6A01114: gnutls_global_init (in /usr/lib/x86_64-linux-gnu/libgnutls.so.26.22.6)
==18109==    by 0x52A6C78: ??? (in /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.3.0)
==18109==    by 0x5285ADC: curl_global_init (in /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.3.0)
==18109==    by 0x663524: git_curl_stream_global_init (curl.c:44)

The test submodule::lookup::duplicated_path, which tries to verify that
we detect submodules with duplicated paths, currently relies on the
gitmodules file of "submod2_target". While this file has two gitmodules
with the same path, one of these gitmodules has an empty name and thus
does not pass `git_submodule_name_is_valid`. Because of this, the test
is in fact dependent on the iteration order in which we process the
submodules. In fact the "valid" submodule comes first, the "invalid"
submodule will cause the desired error. In fact the "invalid" submodule
comes first, it will be skipped due to its name being invalid, and we
will not see the desired error. While this works on the master branch
just right due to the refactoring of our config code, where iteration
order is now deterministic, this breaks on all older maintenance
branches.

Fix the issue by simply using `cl_git_rewritefile` to rewrite the
gitmodules file. This greatly simplifies the test and also makes the
intentions of it much clearer.

Detect duplicated submodules for the same path

When checking whether a rule negates another rule, we were checking
whether a rule had the `GIT_ATTR_FNMATCH_LEADINGDIR` flag set and, if
so, added a "/*" to its end before passing it to `fnmatch`. Our code now
sets `GIT_ATTR_FNMATCH_NOLEADINGDIR`, thus the `LEADINGDIR` flag shall
never be set. Furthermore, due to the `NOLEADINGDIR` flag, trailing
globs do not get consumed by our ignore parser anymore.

Clean up code by just dropping this now useless logic.

When computing whether a file is ignored, we simply search for the first
matching rule and return whether it is a positive ignore rule (the file
is really ignored) or whether it is a negative ignore rule (the file is
being unignored). Each rule has a set of flags which are being passed to
`fnmatch`, depending on what kind of rule it is. E.g. in case it is a
negative ignore we add a flag `GIT_ATTR_FNMATCH_NEGATIVE`, in case it
contains a glob we set the `GIT_ATTR_FNMATCH_HASGLOB` flag.

One of these flags is the `GIT_ATTR_FNMATCH_LEADINGDIR` flag, which is
always set in case the pattern has a trailing "/*" or in case the
pattern is negative. The flag causes the `fnmatch` function to return a
match in case a string is a leading directory of another, e.g. "dir/"
matches "dir/foo/bar.c". In case of negative patterns, this is wrong in
certain cases.

Take the following simple example of a gitignore:

    dir/
    !dir/

The `LEADINGDIR` flag causes "!dir/" to match "dir/foo/bar.c", and we
correctly unignore the directory. But take this example:

    *.test
    !dir/*

We expect everything in "dir/" to be unignored, but e.g. a file in a
subdirectory of dir should be ignored, as the "*" does not cross
directory hierarchies. With `LEADINGDIR`, though, we would just see that
"dir/" matches and return that the file is unignored, even if it is
contained in a subdirectory. Instead, we want to ignore leading
directories here and check "*.test". Afterwards, we have to iterate up
to the parent directory and do the same checks.

To fix the issue, disallow matching against leading directories in
gitignore files. This can be trivially done by just adding the
`GIT_ATTR_FNMATCH_NOLEADINGDIR` to the spec passed to
`git_attr_fnmatch__parse`. Due to a bug in that function, though, this
flag is being ignored for negative patterns, which is fixed in this
commit, as well. As a last fix, we need to ignore rules that are
supposed to match a directory when our path itself is a file.

All together, these changes fix the described error case.