consolidate everything into the repo folder; add compose management comments

All scripts now default BASE to their own directory (SCRIPT_DIR) instead
of ~/docker/ai-stack, so after a git clone the user never needs to change
folders — docker-compose.yml, .env, settings, and data dirs all live next
to the scripts.

configure-searxng-safesearch.sh and configure-storage.sh do the same for
standalone use (still honoured when called with BASE= from a parent script).

docker-compose.yml (generated by both setup scripts) gains a comment block
at the top listing the everyday docker compose commands:
  up -d / down / restart / stop / logs -f / pull / ps
so the file itself is the reference for managing containers.

.gitignore added to exclude generated files (docker-compose.yml, .env,
requirements.txt, helper scripts) and data directories (workspace/, kiwix/,
searxng/, gitea/, etc.) from git tracking.

https://claude.ai/code/session_012gDnantBmFTWZGCiKyjazx

.gitignore

@@ -0,0 +1,24 @@
+# Generated by setup scripts — not tracked
+docker-compose.yml
+.env
+requirements.txt
+mcp_requirements.txt
+start.sh
+stop.sh
+status.sh
+pull-models.sh
+Caddyfile.example
+.ufw-done
+
+# Data directories
+workspace/
+repos/
+papers/
+index/
+logs/
+kiwix/
+gitea/
+portainer-data/
+invokeai-data/
+invokeai-outputs/
+searxng/