Renaming and refactoring basic functions.

- Copy and link functions now just refer to files rather than dotfiles.
- Sourcing custom scrips is now done from one function.
Starting to impliment basic tasks.
Fixing cp helper.
Using rm -rf to remove files instead of unlink.
Handling hook installation and removal better.
Fixing string comparisons.
Removing unused submodule init block.
Changing code style. No functional changes.
Splitting ignored files into a separate list.
Fixing additional conflict options.
Moving all globals to top of script.
Replacing link conflicts by default.
Splitting help into sections.
Fixing hook location.
Fixing prompt fomatting.
Fixing installed hook.
Adding help text for update.
Fixing remove flags.
Formatting replace prompt better (again).
Adding help action to help message.