Now that the index has a "dirty" state, where it has changes that have
not yet been committed or rolled back, our tests need to be adapted to
actually commit or rollback the changes instead of assuming that the
index can be operated on in its indeterminate state.

Test that any changes to the index will mark the index as dirty.  Also
ensure that when we initialize a new index, read the index contents
from disk, or write the index contents to disk that we reset the dirty
flag to zero.  Further ensure that an unforced read with dirty contents
(when the on-disk index has not changed) does _not_ reset the dirty
flag as we have not updated the contents of our index and our unsaved
contents remain intact.

Teach the index when it is "dirty", and has unsaved changes.  Consider
the index dirty whenever a caller has added or removed an entry from the
main index, REUC or NAME section, including when the index is completely
cleared.  Similarly, consider the index _not_ dirty immediately after it
is written, or when it is read from the on-disk index.

This allows us to ensure that unsaved changes are not lost when we
automatically refresh the index.

Don't manipulate the repository's index during stash; instead,
manipulate a temporary index and check it out.

This allows us to use the checkout mechanism to update the workdir and
the repository's index, and allows checkout to use its common mechanisms
to write data and handle errors.

Add tests that ensure that we re-read the on-disk image by default
during checkout, but when the `GIT_CHECKOUT_NO_REFRESH` option is
specified, we do _not_ re-read the index.

Always set the `index` in the `checkout_data`, even in the case that we
are not reloading the index.  Other functionality in checkout examines
the index (for example: determining whether the workdir is modified) and
we need it even in the (uncommon) case that we are not reloading.

When running `git_index_add_all`, we should write the index to disk so
that we can re-read it safely during status.

The index::reuc tests must test that the checkout itself succeeds,
otherwise subsequent tests are not valid.

In fact, the checkouts were failing because when checking out `SAFE`,
they cannot update the files that are in conflict.  Change the checkout
level to `FORCE` to ensure that they get updated correctly.

We add entries into the main index to correspond with the NAME entries
that we're going to test.  NAME entries store the results of conflicts
occuring with rename detection during merge, and they must correspond to
conflicts in the index.

This test was mistakenly adding regular entries.  The checkout
validation failed, since it requires NAME entries to correspond to
high-stage (conflict) entries.  Correct the test to actually create
conflicts.

Fix type confusion in git_smart__connect

Verify ref_pkt's are long enough

If the remote sends a too-short packet, we'll allow `len` to go
negative and eventually issue a malloc for <= 0 bytes on

```
pkt->head.name = git__malloc(alloclen);
```

Nothing verifies that t->refs[0] is a GIT_PKT_REF. A remote can send
another packet type, ultimately resulting in a type confusion in
`git_smart__detect_caps`

Config parser cleanups

Buffers which ran out of memory will never have any memory attached to
them. As such, it is not necessary to call `git_buf_free` if the buffer
is out of memory.

The `parse_variable` function has two out parameters `var_name` and
`var_value`. Currently, those are not being sanitized to `NULL`. when.
any error happens inside of the `parse_variable` function. Fix that.
While at it, the coding style is improved to match our usual coding
practices more closely.

The function `git_config_parse` uses several callbacks to pass data
along to the caller as it parses the file. One design shortcoming here
is that strings passed to those callbacks are expected to be freed by
them, which is really confusing.

Fix the issue by changing memory ownership here. Instead of expecting
the `on_variable` callbacks to free memory for `git_config_parse`, just
do it inside of `git_config_parse`. While this obviously requires a bit
more memory allocation churn due to having to copy both name and value
at some places, this shouldn't be too much of a burden.

Fix last references to deprecated git_buf_free

revwalk: avoid walking the entire history when output is unsorted

Signed-off-by: Sven Strickroth <email@cs-ware.de>

Add mailmap support.

tree: remove unused functions

Link `mbedTLS` libraries in when `SHA1_BACKEND` == "mbedTLS"

editorconfig: allow trailing whitespace in markdown