git_index_entry__init_from_stat: set nsec fields in entry stats

Improve error messages when dirs prevent ref/reflog creation

Support setting custom user-agent

We also keep the "git/1.0" prefix in order to maintain compatibility
with hosters.

We still prefix it with "git/1.0" since that's required in many
situations, but we replace the area which mentions libgit2.

Failing test for case sensitive conflicts in the index

When a non-empty directory exists and prevents the creation of a
reflog, provide a more informative error message.

When a (non-empty) directory exists at the reference target
location, complain with a more actionable error message.

When we insert a conflict in a case-insensitive index, accept the
new entry's path as the correct case instead of leaving the path we
already had.

This puts `git_index_conflict_add()` on the same level as
`git_index_add()` in this respect.

When we're at offset 'i', we're dealing with the 'i+1' stage, since
conflicts start at 1.

Diff: Honor `core.symlinks=false` and fake symlinks

Handle submodules with paths in `git_submodule_update`

Reload the HEAD and index data for a submodule after reading the
configuration.  The configuration may specify a `path`, so we must
update HEAD and index data with that path in mind.

Test that `git_submodule_update` can handle a submodule that is
freshly cloned and has a path differing from its name.

stream: allow registering a user-provided TLS constructor

whitespace.  Collapse spaces around newlines for the summary.

When creating a filebuf, detect a directory that exists in our
target file location.  This prevents a failure later, when we try
to move the lock file to the destination.

Test that on platforms without `core.symlinks`, we preserve symlinks
in `git_index_add_bypath`.  (Users should correct the actual index
entry's mode to change a link to a regular file.)

On platforms that lack `core.symlinks`, we should not go looking for
symbolic links and `p_readlink` their target.  Instead, we should
examine the file's contents.

When `core.symlinks = false`, we write the symlinks content (target)
to a regular file.  We should ensure that when we later see that
regular file, we treat it specially - and that changing that regular
file would actually change the symlink target.  (For compatibility
with Git for Windows).

Fix build for unit test

This allows the application to use their own TLS stream, regardless of
the capabilities of libgit2 itself.

If none of GIT_OPENSSL, GIT_WINHTTP or GIT_SECURE_TRANSPORT
is defined we should also be able to build the unit test.

Use checksums to detect config file changes

Fix build for custom transport users

merge-base: Remove redundant merge bases

This reduces the chances of a crash in the thread tests. This shouldn't
affect general usage too much, since the main usage of these functions
are to read into an empty buffer.