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"];

home/coding/agents/pi.nix

@@ -32,17 +32,19 @@
 
     settings = {
       packages = [
-        "npm:@thesethrose/pi-zai-provider"
-        "npm:pi-mcp-adapter"
-        "npm:pi-subagents"
-        "npm:pi-lens"
-        "npm:pi-web-access"
-        "npm:pi-prompt-template-model"
+        "npm:@dreadedzombie/pi-init"
         "npm:@plannotator/pi-extension"
-        "npm:pi-powerline-footer"
-        "npm:pi-markdown-preview"
-        "npm:pi-tool-display"
+        "npm:@thesethrose/pi-zai-provider"
         "npm:pi-agent-browser-native"
+        "npm:pi-beads-extension"
+        "npm:pi-lens"
+        "npm:pi-markdown-preview"
+        "npm:pi-mcp-adapter"
+        "npm:pi-powerline-footer"
+        "npm:pi-prompt-template-model"
+        "npm:pi-subagents"
+        "npm:pi-tool-display"
+        "npm:pi-web-access"
         "git:github.com/hk-vk/pi-connect"
       ];