Refactor annotations code

[sdsen]

Add following functions

1. gen_comment_stubs_w_src_code() IP: Takes a repo path and commit_id and checkout the code and puts it in src_dir OP: Generates comment stub for the code in src_dir and puts it in op_dir, also takes txl_op_dir
2. gen_human_annotations_from_annotate_src_code(): IP: Takes a repo path and commit_id and checksout the code and puts it in src_dir (optionally the location of src code checked out) OP: JSON format OPENED annotations file for each function in the source code folder
3. gen_opened_annotations_from_src_code(): IP: Takes a repo path and commit_id and checksout the code and puts it in src_dir (optionally the location of src code checked out) OP: JSON format OPENED annotations file for each function in the source code folder.
4. gen_llm_annotations_from_src_code(): IP: Takes a repo path and commit_id and checksout the code and puts it in src_dir (optionally the location of src code checked out) OP: JSON format AI annotations file for each function in the source code folder.