Reworked the whole program. The tree is now file -> dependency -> [file] instead of being file -> file, where the dependency contains all the information to clean up the connection. Extracted some classes to external files, made output more reliable (latex logs for example only get output if they don't produce an output file). Dependencies are now automatically created, however the new system completely destroyed the old readin of config files which should be fixed at some point to make it possible to execute python scripts or gnuplot scripts with parameters (which the program just can't read out by itself).
Added gitignore, removed not needed files in example