feat: add proxyctl daemon manager, fix standalone LS cleanup

- Add proxyctl CLI script for systemd service management
- Add systemd user service file for background operation
- Fix standalone LS kill: properly track real LS PID via pgrep
  and use sudo kill for cross-user cleanup on shutdown
- Remove deprecated scripts (dns-redirect, iptables-redirect,
  mitm-wrapper, standalone-ls, parse-snapshot)
- Disable tool stripping in MITM for tool call investigation
- Update GEMINI.md with CLI tools documentation

src/mitm/modify.rs

@@ -9,7 +9,8 @@ use serde_json::Value;
 use tracing::info;
 
 /// Strip ALL tool definitions.
-const STRIP_ALL_TOOLS: bool = true;
+/// Set to false to allow tools through (for tool call testing).
+const STRIP_ALL_TOOLS: bool = false;
 
 /// Modify a streamGenerateContent request body in-place.
 /// Returns the modified JSON bytes, or None if modification wasn't possible.