Some return codes for functions which may fail are not being checked in
`test_rebase_submodule__initialize`. This may lead us to not notice
errors when initializing the environment and would possibly result in
either memory corruption or segfaults as soon as any of the
initialization steps fails. Fix this by wrapping these function calls
into `cl_git_pass`.

tests: rewrite rebase-submodule .gitmodule file

Fixes #4274

Configuration file fixes with includes

Patch ID calculation

Modifying variables pulled in by an included file currently succeeds,
but it doesn't actually do what one would expect, as refreshing the
configuration will cause the values to reappear. As we are currently not
really able to support this use case, we will instead just return an
error for deleting and setting variables which were included via an
include.

Right now, we have multiple call sites which initialize a `reader`
structure. As the structure is only actually used inside of
`config_read`, we can instead just move the reader inside of the
`config_read` function. Instead, we can just pass in the configuration
file into `config_read`, which eases code readability.

Currently, we only re-parse the top-level configuration file when it has
changed itself. This can cause problems when an include is changed, as
we were not updating all values correctly.

Instead of conditionally reparsing only refreshed files, the logic
becomes much clearer and easier to follow if we always re-parse the
top-level configuration file when either the file itself or one of its
included configuration files has changed on disk. This commit implements
this logic.

Note that this might impact performance in some cases, as we need to
re-read all configuration files whenever any of the included files
changed. It could increase performance to just re-parse include files
which have actually changed, but this would compromise maintainability
of the code without much gain. The only case where we will gain anything
is when we actually use includes and when only these includes are
updated, which will probably be quite an unusual scenario to actually be
worthwhile to optimize.