StreamHandler.reset() was clearing on_content, on_thinking, and on_done
callbacks after every LLM response, but they were only set once per turn.
This caused the thinking indicator and streaming display to stop working
after the first tool call in a multi-step agent turn.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Implement 6 new agent tools — write_file, make_dir, delete_file,
str_replace, patch_apply, run_command — bringing the agent from
read-only observer to active code modifier. All write/shell operations
are gated through the existing permissions service.
Also fix a bug where qwen3.5 thinking mode produces reasoning tokens
but no content after tool results, causing the agent to silently exit.
The loop now detects reasoning-only responses, retries twice, then
injects a nudge message to break the model out of its thinking loop.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
