During my first LLM experiments in Emacs using gptel, I also found that the LLM has considerable difficulties changing source code files with the Unix patch tool.

As Emacs has a built-in tree-sitter package, I implemented this same idea. I created gptel tools like tree_sitter_list_nodes, tree_sitter_get_nodes, tree_sitter_update_nodes, tree_sitter_insert_before_node and tree_sitter_insert_after_node. The "list" tool returns a list of AST nodes with first line number, first line content and node hash. The LLM can then use "get" to collect interesting nodes in their entirety and "update" to update a list of nodes identified by hash with new content (var/function bodies).

Worked like a charm.