Default patterns taking precedence over user-defined ones stops user from fixing some formats.

[head-gardener]

In this comment you say that default patterns take precedence over user-provided ones. This seems like an unusual choice, and in the case of flake.nix files it not only breaks links (github:NixOS/nixpkgs -> https://github.com/github:NixOS/nixpkgs) but also prevents the user from fixing them. I believe it would be better to parse user patterns before default ones.

[head-gardener]

After some tinkering I've narrowed it down to this line, where extra patterns get filtered out unless they come strictly before the default ones - even if they overlap. Replacing start_found with end_found does the trick, ready to send a PR.