Adds a compact `setup --status` view, a `setup --clean` for regenerable
session checkpoints, and `--tools`/`--plugins` scaffolding for
~/.deepseek/{tools,plugins} so the extension model has a documented home
that doctor can count. `doctor --json` lands as a CI-safe alternative to
the human-readable doctor (skips the live API probe).
Also locks down the engine's hostility to fake tool-call wrappers:
filter_tool_call_delta and the marker constants are now testable, the
streaming loop emits one compact status notice per turn when it strips
a wrapper, and a new protocol_recovery integration test asserts that
the legacy text parser never turns <function_calls> into a real tool
call. Adds 23 unit tests + 14 integration tests covering both slices.
Adds first-class DeepSeek V4 Pro and Flash support, updates the default model to deepseek-v4-pro, aligns legacy aliases with the current V4 1M context behavior, and fixes thinking-mode request handling.
Key fixes:
- Send DeepSeek's raw Chat Completions `thinking` parameter at the top level instead of SDK-only `extra_body`.
- Preserve assistant `reasoning_content` for all prior thinking-mode tool-call turns so subsequent requests satisfy DeepSeek V4's replay requirement.
- Fix npm wrapper concurrent first-run downloads by using per-process temporary download paths.
- Add `.mailmap` so historical bot-attributed commits aggregate under Hunter Bown where mailmap is honored.
Verified with the full local Rust gate, live DeepSeek V4 smoke, npm wrapper temp-install smoke, and green PR CI across Linux, macOS, and Windows.
Keep legacy /normal and settings fallback behavior mapped to Agent, align docs around the three visible modes, and include the current TUI and onboarding refinements in this worktree.
- Move src/* into crates/tui/src/ to create a proper workspace structure
- Add .claude/ and .trimtab/ directories for Trimtab closed-loop workflow
- Add DEPENDENCY_GRAPH.md and update documentation
- Update Cargo.toml files to reflect new crate dependencies
- Update CI workflows and npm package scripts
- All tests pass, release build works
Major Features:
- Runtime API for external integrations and turn management
- Task manager with persistence and recovery
- Shell output streaming and improved tool execution
- Error taxonomy and audit logging
- Command palette and UI enhancements
Documentation:
- Runtime API documentation
- Operations runbook
- Architecture updates
Fixes:
- Auto-compaction threshold and triggering logic
- Doctor command API key validation
- Clippy and formatting compliance
Hunter Bown