Failing test for case sensitive conflicts in the index

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.

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.

Instead of relying on the size and timestamp, which can hide changes
performed in the same second, hash the file content's when we care about
detecting changes.

We currently use the timestamp in order to decide whether a config file
has changed since we last read it.

This scheme falls down if the file is written twice within the same
second, as we fail to detect the file change after the first read in
that second.

index: read_index must update hashes

We should explicitly include the declaration of git_strarray
from "include/git2/sys/transport.h"

Fix segfault when reading reflog with extra newlines

Using calloc instead of malloc because the parse error will lead to an immediate free of committer (and its properties, which can segfault on free if undefined - test_refs_reflog_reflog__reading_a_reflog_with_invalid_format_returns_error segfaulted before the fix).

#3458

pool: Simplify implementation