Change midx.c and midx-write.c to not use global variables

Similar to the earlier patch series on cleaning up packfile.c and removing usage of global variables 1, we change the midx.c and midx-write.c files to no longer use global variables.

This is done by the following:

• Usage of repository variable already available in existing structs.
• Passing down repository variable from other subsystems.
• Modifying all subcommands to obtain repository variable from the command in builtins/ and passing down the variable from there.

The biggest change here being commit 5, wherein we modify all subcommands to add the repository variable. Since the subcommand definition are not often changed, it shouldn't cause too many conflicts with in flight topics.

Since the packfile.c cleanup is still in flight, this series is based on top of master: b31fb630 (Merge https://github.com/j6t/git-gui, 2024-11-11) with those patches merged in.

Closes #374 (closed)