chore: complete AGENTS.md documentation

- Add comprehensive project documentation to AGENTS.md
- Remove stale docs from docs/ directory
- Update agent configs (agents.nix, pi.nix)
- Update python.nix language config
- Update .gitignore

home/coding/agents/agents.nix

@@ -63,7 +63,8 @@
   home.packages = with pkgs; [
     agenix-cli
     agent-browser
-    pyrefly
+    beads
+    pi
     (qmd.override {
       vulkanSupport = videoDrivers == ["amdgpu"];
       cudaSupport = videoDrivers == ["nvidia"];