checkout: fix test fixture missing objects

The testrepo test fixture has an index file that's damaged, missing an
object.  The index previously had an entry of `src/index.c` with id
3161df8cbf3a006b4ef85be6497a0ea6bde98541, but that object was missing in
the repository.  This commit adds an object to the repository and
updates the index to use that existing blob.

Similarly, the index has an entry for `readme` with an id of
97328ac7e3bd0bcd3900cb3e7a624d71dd0df888.  This can be restored from
other test repositories.

With these fixed, now the write tree from index tests can pass since they
validate object existence.