Exclude some of the changed files

[hkdobrev]

Exclude changed files detected from Git if:

• they have been deleted and not in the worktree
• they are changed in submodules

Both of these scenarios have some valid use cases for running commands on changes. E.g. refreshing a build after deleting files.
However, they are rare. E.g.:

• If a file the command expects is now missing, the command may fail.
• If a submodule is changed, a command might run unnecessarily.

⚠️ If there are users who would like these changes to still trigger command run, I think it's best done behind a configuration.
👉 But the default behaviour should not be surprising and all of the use cases in the readme describe cases where these changes should not trigger command runs.