feat: hippocampal memory system, improved tool/subagent error messages, YOLO mode cleanup

Cargo.toml

@@ -8,6 +8,7 @@ members = [
     "crates/execpolicy",
     "crates/hooks",
     "crates/mcp",
+    "crates/memory",
     "crates/protocol",
     "crates/release",
     "crates/secrets",

crates/memory/Cargo.toml

@@ -0,0 +1,19 @@
+[package]
+name = "codewhale-memory"
+version.workspace = true
+edition.workspace = true
+license.workspace = true
+repository.workspace = true
+description = "Hippocampal memory system — structured entity graph with cross-session recall"
+
+[dependencies]
+anyhow.workspace = true
+chrono.workspace = true
+rusqlite.workspace = true
+serde.workspace = true
+serde_json.workspace = true
+sha2.workspace = true
+uuid.workspace = true
+
+[dev-dependencies]
+tempfile = "3"

crates/memory/src/lib.rs

@@ -0,0 +1,29 @@
+//! # Codewhale Hippocampal Memory System
+//!
+//! A structured, SQLite-backed memory store that enables the agent to remember
+//! facts, entities, and relationships across sessions — the foundation for
+//! true infinite-context and cross-session recall.
+//!
+//! ## Core Concepts
+//!
+//! - **Entities**: Files, PRs, issues, concepts, people, decisions — anything
+//!   the model might need to reference later.
+//! - **Relations**: Directed edges connecting entities (e.g. `dispatch.rs` is
+//!   `part_of` `PR #2933`).
+//! - **Facts**: Standalone factual statements, optionally bound to an entity.
+//!   Stored with an importance score (0.0–1.0) for active forgetting.
+//!
+//! ## Usage
+//!
+//! ```rust,ignore
+//! use codewhale_memory::MemoryStore;
+//!
+//! let store = MemoryStore::open(&path)?;
+//! store.insert_fact(None, "user prefers 4-space indentation", "user", 0.9, None)?;
+//! let facts = store.search_facts("indentation", 10)?;
+//! ```
+
+pub mod schema;
+pub mod store;
+
+pub use store::{Entity, Fact, MemoryStore, Relation};

crates/memory/src/schema.rs

@@ -0,0 +1,80 @@
+//! SQLite schema for the hippocampal memory store.
+//!
+//! Three core tables:
+//!
+//! - **`entities`**: A "thing" the model might need to remember — a file path,
+//!   an issue number, a PR, a person, a concept, a decision.
+//! - **`relations`**: A directed edge connecting two entities. The `kind` field
+//!   says what the relationship means (e.g. `"fixes"`, `"part_of"`, `"depends_on"`).
+//! - **`facts`**: A standalone statement about something the model learned. May
+//!   reference an entity via `entity_id`.
+
+use rusqlite::Connection;
+
+/// Create all tables if they don't exist.
+pub(crate) fn migrate(conn: &Connection) -> rusqlite::Result<()> {
+    conn.execute_batch(
+        "
+        CREATE TABLE IF NOT EXISTS entities (
+            id          TEXT PRIMARY KEY,
+            kind        TEXT NOT NULL,         -- 'file', 'issue', 'pr', 'concept', 'decision', 'person', 'config'
+            name        TEXT NOT NULL,         -- human-readable label
+            description TEXT NOT NULL DEFAULT '',
+            created_at  TEXT NOT NULL DEFAULT (datetime('now')),
+            updated_at  TEXT NOT NULL DEFAULT (datetime('now'))
+        );
+
+        CREATE INDEX IF NOT EXISTS idx_entities_kind   ON entities(kind);
+        CREATE INDEX IF NOT EXISTS idx_entities_name   ON entities(name);
+
+        CREATE TABLE IF NOT EXISTS relations (
+            id            TEXT PRIMARY KEY,
+            source_id     TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE,
+            target_id     TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE,
+            kind          TEXT NOT NULL,       -- 'fixes', 'part_of', 'depends_on', 'contains', 'references', 'implements'
+            strength      REAL NOT NULL DEFAULT 1.0,  -- 0.0–1.0 confidence/importance
+            created_at    TEXT NOT NULL DEFAULT (datetime('now')),
+            session_id    TEXT,                 -- which session created this relation
+            UNIQUE(source_id, target_id, kind)
+        );
+
+        CREATE INDEX IF NOT EXISTS idx_relations_source ON relations(source_id);
+        CREATE INDEX IF NOT EXISTS idx_relations_target ON relations(target_id);
+        CREATE INDEX IF NOT EXISTS idx_relations_kind   ON relations(kind);
+
+        CREATE TABLE IF NOT EXISTS facts (
+            id          TEXT PRIMARY KEY,
+            entity_id   TEXT REFERENCES entities(id) ON DELETE SET NULL,
+            content     TEXT NOT NULL,          -- the factual statement
+            source      TEXT NOT NULL DEFAULT '', -- where this fact came from (tool call, session, user)
+            importance  REAL NOT NULL DEFAULT 0.5,  -- 0.0–1.0
+            created_at  TEXT NOT NULL DEFAULT (datetime('now')),
+            session_id  TEXT
+        );
+
+        CREATE INDEX IF NOT EXISTS idx_facts_entity   ON facts(entity_id);
+        CREATE INDEX IF NOT EXISTS idx_facts_importance ON facts(importance DESC);
+
+        -- Full-text search over facts (enables pattern-completion-like queries)
+        CREATE VIRTUAL TABLE IF NOT EXISTS facts_fts USING fts5(
+            content,
+            content=facts,
+            content_rowid=rowid
+        );
+
+        -- Triggers to keep FTS index in sync
+        CREATE TRIGGER IF NOT EXISTS facts_ai AFTER INSERT ON facts BEGIN
+            INSERT INTO facts_fts(rowid, content) VALUES (new.rowid, new.content);
+        END;
+
+        CREATE TRIGGER IF NOT EXISTS facts_ad AFTER DELETE ON facts BEGIN
+            INSERT INTO facts_fts(facts_fts, rowid, content) VALUES('delete', old.rowid, old.content);
+        END;
+
+        CREATE TRIGGER IF NOT EXISTS facts_au AFTER UPDATE ON facts BEGIN
+            INSERT INTO facts_fts(facts_fts, rowid, content) VALUES('delete', old.rowid, old.content);
+            INSERT INTO facts_fts(rowid, content) VALUES (new.rowid, new.content);
+        END;
+        ",
+    )
+}