Yellow squiggly lines begone!
Done automatically on .cpp files through `run-clang-tidy`, with manual corrections to the mistakes.
If an import is directly used, but is technically unnecessary since it's recursively imported by something else, it is *not* removed.
The tool doesn't touch .h files, so I did some of them by hand while fixing errors due to old recursive imports.
Not everything is removed, but the cleanup should be substantial enough.
Because this done on Linux, code that isn't used on it is mostly untouched.
(Hopefully no open PR is depending on these imports...)

Aside from allowing users to persistently set the window to their
desired size, this is also necessary to allow saving of the splitter
positions in FIFOAnalyzer to work correctly.

Follow-up for
https://github.com/dolphin-emu/dolphin/pull/12918#discussion_r1785153070.

This reverts the revert commit bc67fc97c39628c76a4dbca411b0e8a9bfaf726a,
except for the changes in BaseConfigLoader.cpp, which caused the bug
that made us revert 72cf2bdb87f09deff22e1085de3290126aa4ad05. PR 12917
contains an improved change to BaseConfigLoader.cpp, which can be merged
(or rejected) independently.

A few changes have also been made based on review comments.

Most of these changes are to improve consistency in capitalization.

This reverts commit 72cf2bdb87f09deff22e1085de3290126aa4ad05.

SYSCONF settings are getting cleared when they shouldn't be. Let's
revert the change until I get proper time to figure out why it's broken.

Some pieces of code are calling IsRunning because there's some
particular action that only makes sense when emulation is running, for
instance showing the state of the emulated CPU. IsRunning is appropriate
to use for this. Then there are pieces of code that are calling
IsRunning because there's some particular thing they must avoid doing
e.g. when the CPU thread is running or IOS is running. IsRunning isn't
quite appropriate for this. Such code should also be checking for the
states Starting and Stopping. Keep in mind that:

* When the state is Starting, the state can asynchronously change to
  Running at any time.
* When we try to stop the core, the state gets set to Stopping before we
  take any action to actually stop things.

This commit adds a new method Core::IsUninitialized, and changes all
callers of IsRunning and GetState that look to me like they should be
changed.