Refactoring, reformatting, documentation, patch detection, placeholder.

- Removed automake files from .gitignore. Whew.
- Changed file include logic. (WIP)
- Added more giant code documentation comments.
- New isPatch() function to detect if a file is a patch or not.
- New useFile() function to simplyify code structure.
- Changed some incorrect return values.
- Added messages to patch checking functions for each format. (WIP)
- Placeholder UPSReadRecord function added. (WIP)
- Reformatted some code.
Changed ipsFile -> patchFile for code readability.
Moved patch checking logic, File paramaters can now be in any order.

- Updated AIPS.c to allow patch file and ROM file arguments to come in
any order with intelligent checking.
- Moved Patch file validity checking to file inclusion step, and not the
patching step...
- Made more functions utilize returns as opposed to assigning to a
random pointer for cleanliness sake.
Modified verbosity, and added new verbosity level.

- Removed verbosity for normal functionality (Need -v to see information now.)
- Added new verbosity level. (-v -v adds more verbosity)
- Patching debug information put in veryverbose.
- Updated help screen.