Change: Prevent excluding paths explicitly passed to `backup`

When e.g. `restic backup --exclude-if-present .git /home/user/data` was run
and `/home/user/.git` existed, restic excluded the `data` directory from the
snapshot. The same applied to `--exclude-caches` or `--one-file-system`.

Similarly, `restic backup --exclude-larger-than 1M large-file.bin` produced
an empty snapshot when the file was larger than one megabyte.

The `backup` command now tracks which files and directories were specified on
the command line and does not apply excludes to those paths. Content inside a
backed-up directory is still filtered by excludes as before.

https://github.com/restic/restic/issues/5767
https://github.com/restic/restic/pull/21797
