Fix the file-mode test to expect system umask being applied to the
created file as well (it is currently applied to the directory only).
This fixes the test on systems where umask != 022.

Signed-off-by: Michał Górny <mgorny@gentoo.org>

tree: mark cloned tree entries as un-pooled

When duplicating a `struct git_tree_entry` with
`git_tree_entry_dup` the resulting structure is not allocated
inside a memory pool. As we do a 1:1 copy of the original struct,
though, we also copy the `pooled` field, which is set to `true`
for pooled entries. This results in a huge memory leak as we
never free tree entries that were duplicated from a pooled
tree entry.

Fix this by marking the newly duplicated entry as un-pooled.

Improvements to tree parsing speed

Compiler warning fixes

Return an error in case the length is too big. Also take this
opportunity to have a single allocating function for the size and
overflow logic.

Recursive Merge

This reduces the size of the struct from 32 to 26 bytes, and leaves a
single padding byte at the end of the struct (which comes from the
zero-length array).

We already know the size due to the `memchr()` so use that information
instead of calling `strlen()` on it.

These are rather small allocations, so we end up spending a non-trivial
amount of time asking the OS for memory. Since these entries are tied to
the lifetime of their tree, we can give the tree a pool so we speed up
the allocations.

We've already looked at the filename with `memchr()` and then used
`strlen()` to allocate the entry. We already know how much we have to
advance to get to the object id, so add the filename length instead of
looking at each byte again.

When building a recursive merge base, allow conflicts to occur.
Use the file (with conflict markers) as the common ancestor.

The user has already seen and dealt with this conflict by virtue
of having a criss-cross merge.  If they resolved this conflict
identically in both branches, then there will be no conflict in the
result.  This is the best case scenario.

If they did not resolve the conflict identically in the two branches,
then we will generate a new conflict.  If the user is simply using
standard conflict output then the results will be fairly sensible.
But if the user is using a mergetool or using diff3 output, then the
common ancestor will be a conflict file (itself with diff3 output,
haha!).  This is quite terrible, but it matches git's behavior.

Use annotated commits to act as our virtual bases, instead of regular
commits, to avoid polluting the odb with virtual base commits and
trees.  Instead, build an annotated commit with an index and pointers
to the commits that it was merged from.

When there are more than two common ancestors, continue merging the
virtual base with the additional common ancestors, effectively
octopus merging a new virtual base.

When the commits to merge have multiple common ancestors, build a
"virtual" base tree by merging the common ancestors.

Add a simple recursive test - where multiple ancestors exist and
creating a virtual merge base from them would prevent a conflict.

Memleak fixes

checkout: only consider nsecs when built that way

When examining the working directory and determining whether it's
up-to-date, only consider the nanoseconds in the index entry when
built with `GIT_USE_NSEC`.  This prevents us from believing that
the working directory is always dirty when the index was originally
written with a git client that uinderstands nsecs (like git 2.x).

Fix <0 unsigned comparison (stat.st_size should be an off_t)

Fix some warnings

Stat fixes