Parse files one at a time in EnemyGroupManager

Loading enemy files to read enemygroup information was done by
essentially concatenating all of the enemy files together. This broke
the ability to overwrite that data via the same file across mods.

Instead, we now get a list of all the enemy files and parse each one
individually.
Implement more consistent file parsing method

Closes #1040

Now by default, all mod files will overwrite eachother. For files that
were automatically concatenated before, they can still be concatenated
by making the first line of all but the first file "APPEND". For
example, we can combine the credits for the engine, fantasycore, and
alpha_demo by adding "APPEND" to the top of the credits cutscene files
in fantasycore and alpha_demo.
Remove usage of Quest index

Instead of reading quests/index.txt to find out which quests files to
load, we now just grab all the files in quests/. This is consistent with
how we load enemies in EnemyGroupManager, and means one less file for
modders to worry about.
Merge pull request #1066 from dorkster/fileparser

FileParser improvments