Add Directory Processing and Patch Output Generation

[Yiannis128]

This PR will implement a refactor of a few base systems, along with the functionality to process entire directories. The refactor implements the Solution class that allows to handle multiple files using SourceFile. SourceFile also supports tracking of history of patches and verifier output for each patch.

The PR also adds the ability to output the changes to fixed source code in diff format.

TODO

• Write solution.py tests
• Better output formatting for when processing directories (currently just prints all output without any separation)
• esbmc_load_source_code should use save_file from SourceFiles.