Add license text.

The full text should be distributed and not just the header added to
source files.
Remove generated files that shouldn't be in VCS.
Update gitignore file.
doc: Remove pdfsync package from documentation.

All TeX processors support SyncTeX and pdfsync is super outdated.
doc: Replace deprecated subfigure package.

Similar functionality is provided by the subcaption package, which is a
part of the caption package.
doc: Use TitleCase instead of ugly ALLCAPS.
doc: Use geometry package to set page size.
doc: Set input as utf8, not latin9, whatever that is.
doc: Add macros for easy styling of program names.
doc: Remove unnecessarily forced newlines.
doc: Use braces to simplify font size changes.
doc: Use listings package more effectively.

Essentially, it provides a verbatim environment, which greatly reduces
the amount of escaping that needs to be done. Plus, one can make fancy
boxes around code and stuff.
doc: Use hyperref's autoref macro for better links.
doc: Tweak figure layout and some text formatting.
doc: Use description lists where possible.
doc: Remove old hyperref settings.
doc: Fix some bbox warnings.
doc: Update PDF manual.
Merge pull request #5 from QuLogic/doc

Documentation Cleanup