refactor: consolidate hypotheses, agent_signals, and process_logs into action-based smart tools

server/src/instructions.md

@@ -68,6 +68,19 @@ The server consolidates granular single-purpose tools into domain-named smart to
   - `action: "read"`: Read OS clipboard.
   - `action: "write"`: Write text/html/files/image to clipboard.
 
+* **`hypotheses`**: Diagnostic hypothesis memory.
+  - `action: "log"`: Record diagnostic hypothesis (requires `hypothesis`, optional `status: "open" | "verified" | "disproven"`, `evidence: Vec<String>`, `test_command`, `git_branch`, `repo_name`).
+  - `action: "query"`: Query hypotheses (optional `status`, `git_branch`, `repo_name`).
+
+* **`agent_signals`**: Inter-agent signal bus.
+  - `action: "broadcast"`: Broadcast signal to other agents (requires `signal_type`, `payload`, optional `target_agent`, `ttl_seconds`).
+  - `action: "query"`: Query active signals (optional `signal_type`, `include_expired: bool`).
+
+* **`process_logs`**: Process and daemon log management.
+  - `action: "watch"`: Register or update log file watcher (requires `label`, `file_path`, optional `description`).
+  - `action: "get"`: Retrieve recent log lines from watched process log (requires `label`, optional `tail_lines: usize`).
+  - `action: "clear"`: Clear or truncate watched process log file (requires `label`).
+
 ---
 
 ## 3. VCS & SVN Agnosticism & Multi-Repo Provenance
@@ -180,16 +193,16 @@ To maintain maximum security, speed, and cross-platform reliability:
 * **Batch Vector Indexing & Similarity Score Guidance**: `VectorDB` provides `index_documents_batch` for single-request multi-point vector upserts and explicit score calibration notes ($\ge 0.75$ high confidence match).
 * **Compact JSON MCP Resources & UTF-8 Activity Truncation**: MCP resources serialize using compact JSON (`to_string`), `TerminalHistoryResource` / `MilestonesResource` enforce output bounds, and `format_tool_activity_description` uses `floor_char_boundary` for guaranteed UTF-8 safety.
 * **SIMD-Friendly Single-Pass Cosine Similarity**: `cosine_similarity` calculates dot product and Euclidean norm squares in a single linear pass over float vectors, enabling SIMD compiler auto-vectorization.
-* **Safe Stream Decoding on Log Tails**: Log tail operations (`get_recent_logs`) read raw bytes and decode using lossy UTF-8 conversion (`String::from_utf8_lossy`) to ensure resilience when seeking across multi-byte UTF-8 boundaries.
+* **Safe Stream Decoding on Log Tails**: Log tail operations (`process_logs`, action: "get") read raw bytes and decode using lossy UTF-8 conversion (`String::from_utf8_lossy`) to ensure resilience when seeking across multi-byte UTF-8 boundaries.
 * **Task Summary UTF-8 Truncation Safety**: `tasks` tool (`action = "list"`) truncates serialized task text strictly along UTF-8 character boundaries using `floor_char_boundary` when enforcing `max_tokens`.
 * **Sequential Snapshot Lock Scope Flattening**: `GenerateStandupReportHandler` reads `tasks`, `ledger`, and `session_summaries` sequentially rather than nesting read locks, preventing multi-lock deadlocks during concurrent store modifications.
 * **Directory Tree Depth Safeguard**: `ReadDirectoryArchitectureHandler` caps directory recursion at depth 10 to prevent stack overflow on deep or cyclic directory structures.
 * **Deterministic Total-Order Score Ranking**: `OmniSearchHandler` uses `f64::total_cmp` for Reciprocal Rank Fusion (RRF) score sorting, guaranteeing deterministic NaN-safe search result ordering.
 * **RPC Timeout Memory Hygiene**: `nvim-core` maintains request hygiene by removing pending request entries from static RPC maps upon timeout or channel drop, eliminating orphan memory leaks.
 * **Embedding Input Safeguard**: `generate_embedding_async` returns explicit errors for empty/0-length text inputs instead of returning empty vectors, preventing downstream vector dimension mismatches during cosine similarity calculations.
-* **Path Traversal Security Guards**: `validate_safe_path` enforces path canonicalization and rejects relative parent traversal components (`..`) across file and process log handlers (`GetRecentLogsTool`, `WatchProcessLogsTool`).
+* **Path Traversal Security Guards**: `validate_safe_path` enforces path canonicalization and rejects relative parent traversal components (`..`) across file and process log handlers (`process_logs` / `ProcessLogsTool`).
 * **Watcher Map Memory Eviction**: Proactive daemon file watcher in `watcher.rs` caps `last_processed` map size at 1,000 entries and purges entries older than 10 minutes to prevent monotonic memory leakage.
-* **Comprehensive Serde Casing Aliases**: All 8 consolidated tool action enums (TaskAction, MilestoneAction, SnippetAction, DecisionAction, TechDebtAction, EnvAction, ClipboardAction, HandoffMemoAction) include serde alias attributes supporting `snake_case`, `camelCase`, `PascalCase`, and uppercase variants for maximum LLM casing resilience.
+* **Comprehensive Serde Casing Aliases**: All 11 consolidated tool action enums (TaskAction, MilestoneAction, SnippetAction, DecisionAction, TechDebtAction, EnvAction, ClipboardAction, HandoffMemoAction, HypothesisAction, AgentSignalAction, ProcessLogAction) include serde alias attributes supporting `snake_case`, `camelCase`, `PascalCase`, and uppercase variants for maximum LLM casing resilience.
 * **Two-Phase Graph Condensation**: `condense_graph_worker` uses a 2-phase commit (non-destructive `read_with` -> graph insert -> prune by timestamp/content) to prevent data loss if summarization or graph insertion fails.
 * **Store Write Lock Minimization**: `Store::modify` and `Store::modify_async` unblock concurrent readers during JSON serialization by releasing the write lock immediately after mutating memory state.
 * **Redb Database Lock Retry Backoff**: `init_db` retries transient Redb lock contention with exponential backoff (3 attempts, 150ms delay) before falling back.