nlm-memory 0.5.21 → 0.5.22

package/README.md

@@ -79,15 +79,15 @@ One corpus across every adapter. MCP works against all nine. **Automatic context
 
 | Runtime | Connect | Sessions read from | Hooks |
 |---|---|---|---|
-| **Claude Code** | `nlm connect claude-code` | `~/.claude/projects/**/*.jsonl` | 5 (UserPromptSubmit, SessionStart, Stop, PreCompact, SubagentStart) |
-| **Codex CLI** | `nlm connect codex` | `~/.codex/sessions/` | Marketplace plugin |
-| **Hermes** | `nlm connect hermes` | Hermes session DB | MCP only |
-| **Hermes Agent** | `nlm connect hermes-agent` | Hermes plugin path | pre-turn, post-turn, lifecycle |
+| **Claude Code** | `nlm connect claude-code` | `~/.claude/projects/**/*.jsonl` | 6 hooks: UserPromptSubmit, SessionStart, SessionEnd, Stop, PreCompact, SubagentStart |
+| **Codex CLI** | `nlm connect codex` | `~/.codex/sessions/` | Marketplace plugin (UserPromptSubmit + Stop) |
+| **Hermes** | `nlm connect hermes` | `~/.hermes/sessions/` | MCP only |
+| **Hermes Agent** | `nlm connect hermes-agent` | `~/.hermes/state.db` | 6 hooks: pre_llm_call, post_llm_call, on_session_start/end/finalize/reset |
 | **Cursor** | `nlm connect cursor` | Cursor IDE chat DB | MCP only |
 | **Windsurf** | `nlm connect windsurf` | Windsurf user dir | MCP only |
 | **OpenCode** | adapter active | `~/.local/share/opencode/` | MCP only |
 | **Aider** | adapter active | `AIDER_CHAT_HISTORY_FILE` | MCP only |
-| **pi.dev** | `nlm setup` (auto) or `nlm connect pi` | `~/.pi/agent/sessions/**/*.jsonl` | input (prompt-recall) |
+| **pi.dev** | `nlm setup` (auto) or `nlm connect pi` | `~/.pi/agent/sessions/**/*.jsonl` | 1 hook: input (prepend via transform) |
 
 `nlm disconnect <runtime>` reverses any of the above.
 
@@ -99,19 +99,37 @@ Two delivery paths. They share the same index.
 
 ### 1. Hooks — automatic context injection
 
-Hooks fire on user input and prepend a pointer block of likely-relevant prior sessions to the model's context. Three runtimes ship them today: Claude Code (full five-hook lifecycle), Hermes Agent (parallel set), and pi.dev (one `input` hook via [nlm/](nlm/README.md), wired by `nlm setup` or `nlm connect pi`). Full lifecycle, modes, logging surface, and the load-bearing daily liveness canary documented in [docs/hooks.md](docs/hooks.md).
+Hooks fire on user input and prepend a pointer block of likely-relevant prior sessions to the model's context. Three runtimes ship hooks today: Claude Code (six-hook lifecycle), Hermes Agent (six parallel hooks), and pi.dev (one `input` hook via [nlm/](nlm/README.md)). On all other runtimes the agent calls `recall_sessions` explicitly via MCP. Full lifecycle, modes, logging surface, and the daily liveness canary documented in [docs/hooks.md](docs/hooks.md).
 
-The Claude Code surface (the most complete) installs five hooks into `~/.claude/settings.json`:
+**Claude Code** — six hooks written to `~/.claude/settings.json` via `nlm connect claude-code`:
 
 | Event | What NLM does | Mode |
 |---|---|---|
 | **UserPromptSubmit** | Score the prompt, silently prepend pointer block listing 0–3 most likely-relevant prior sessions | live by default |
 | **SessionStart** | Cold-start agents (cron, background) hit this; same pointer-block delivery without a user prompt | live by default |
+| **SessionEnd** | Delete the per-conversation memo on session close so state files don't accumulate | always on |
 | **Stop** | Scan the model's response for citations of surfaced session IDs → updates `useful_hit_rate` and builds the reranker training substrate | always on |
 | **PreCompact** | Flush the per-conversation surfaced-IDs memo so post-compaction recalls aren't gated | always on |
 | **SubagentStart** | Record parent→subagent links so threads stay coherent across dispatches | always on |
 
-Switch to **shadow** mode (log-only, no injection) anytime with `NLM_HOOK_MODE=shadow` on the hook command. Toggle for an existing install: re-run `nlm hook install` after changing the env var. The hook fails open — any error yields a clean exit and never blocks the model.
+**Hermes Agent** — six hooks installed to `~/.hermes/plugins/nlm-memory/` via `nlm connect hermes-agent`. All calls are fire-and-forget except `pre_llm_call`, which returns a context string for injection:
+
+| Hook | What NLM does | Blocks turn? |
+|---|---|---|
+| **pre_llm_call** | POST prompt to daemon → inject pointer block of relevant prior sessions into context | yes (returns context string) |
+| **post_llm_call** | POST assistant response to daemon → citation scan, `useful_hit_rate` update | no |
+| **on_session_start** | Signal session open → daemon initialises per-session memo | no |
+| **on_session_end** | Signal session close → daemon flushes memo | no |
+| **on_session_finalize** | Signal transcript finalised → triggers async classifier run | no |
+| **on_session_reset** | Signal session reset → daemon clears per-session state | no |
+
+**pi.dev** — one `input` hook registered via `nlm connect pi`. Pi's extension API only exposes `input`, so transcript ingestion is handled separately by the passive adapter scanning `~/.pi/agent/sessions/`:
+
+| Hook | What NLM does | Blocks turn? |
+|---|---|---|
+| **input** | Score user message → if relevant sessions found, prepend pointer block to the prompt text via `{ action: "transform" }` | yes (returns transformed text) |
+
+All three fail-open: any daemon error yields a clean exit and never blocks the model. Switch Claude Code hooks to **shadow** mode (log-only, no injection) with `NLM_HOOK_MODE=shadow`.
 
 ### 2. MCP — explicit tools any agent can call
 

package/dist/core/actions/overlay.d.ts

@@ -15,10 +15,25 @@ export interface ActionOverlay {
     readonly retiredEntities: Set<string>;
     readonly snoozedEntities: Map<string, string>;
     readonly labeledEntities: Map<string, string>;
+    /** entity canonical → new display label. Storage canonical is untouched;
+     *  legacy-name recall still resolves because sessions stay tagged with
+     *  the original canonical. Last non-reverted rename per subject wins. */
+    readonly renamedEntities: Map<string, string>;
     /** open-question ids resolved without becoming decisions */
     readonly resolvedOpens: Set<string>;
     /** open-question id → resolution text (becomes a decision at projection time) */
     readonly promotedOpens: Map<string, string>;
+    /** decision ids hidden from the projection (the underlying session body keeps the original line). */
+    readonly dismissedDecisions: Set<string>;
+    /** decision id → corrected text shown in place of the original. */
+    readonly revisedDecisions: Map<string, string>;
+    /** entity canonical → user-asserted coherence bucket. Overrides the
+     *  computed (session_count + age) classification at projection time;
+     *  last non-reverted write wins. */
+    readonly coherenceOverrides: Map<string, "active" | "sparse" | "stale">;
+    /** source canonical → target canonical. Source is hidden at projection
+     *  time (treated as retired); target absorbs the source's session count. */
+    readonly mergedEntities: Map<string, string>;
 }
 export declare const EMPTY_OVERLAY: ActionOverlay;
 export declare function loadActionOverlay(db: Database.Database): ActionOverlay;
@@ -28,3 +43,10 @@ export declare function loadActionOverlay(db: Database.Database): ActionOverlay;
  * subject_ids round-trip.
  */
 export declare function openQuestionId(sessionId: string, text: string): string;
+/**
+ * Stable id for a decision: `${sessionId}::dec::${hash12(text)}`. Same
+ * deterministic-hash trick as open questions; the `dec::` infix keeps the
+ * two ID spaces disjoint so a decision and an open question with the same
+ * text in the same session don't collide.
+ */
+export declare function decisionId(sessionId: string, text: string): string;

package/dist/core/actions/overlay.js

@@ -14,8 +14,13 @@ export const EMPTY_OVERLAY = {
     retiredEntities: new Set(),
     snoozedEntities: new Map(),
     labeledEntities: new Map(),
+    renamedEntities: new Map(),
     resolvedOpens: new Set(),
     promotedOpens: new Map(),
+    dismissedDecisions: new Set(),
+    revisedDecisions: new Map(),
+    coherenceOverrides: new Map(),
+    mergedEntities: new Map(),
 };
 export function loadActionOverlay(db) {
     const hasActions = db
@@ -29,14 +34,22 @@ export function loadActionOverlay(db) {
         retiredEntities: new Set(),
         snoozedEntities: new Map(),
         labeledEntities: new Map(),
+        renamedEntities: new Map(),
         resolvedOpens: new Set(),
         promotedOpens: new Map(),
+        dismissedDecisions: new Set(),
+        revisedDecisions: new Map(),
+        coherenceOverrides: new Map(),
+        mergedEntities: new Map(),
     };
+    // ORDER BY id keeps reducer deterministic: later writes overwrite earlier
+    // ones, so the latest non-reverted rename per subject wins.
     const rows = db
         .prepare(`
       SELECT kind, subject_type, subject_id, payload
       FROM actions
       WHERE reverted_by IS NULL
+      ORDER BY id
     `)
         .all();
     const now = new Date().toISOString();
@@ -63,6 +76,13 @@ export function loadActionOverlay(db) {
             if (newType)
                 overlay.labeledEntities.set(r.subject_id, newType);
         }
+        else if (r.kind === "rename_entity" && r.subject_type === "entity") {
+            const to = typeof payload?.["to"] === "string" ? payload["to"].trim() : "";
+            if (to && to !== r.subject_id)
+                overlay.renamedEntities.set(r.subject_id, to);
+            else
+                overlay.renamedEntities.delete(r.subject_id);
+        }
         else if (r.kind === "resolve_open" && r.subject_type === "open_question") {
             overlay.resolvedOpens.add(r.subject_id);
         }
@@ -71,6 +91,33 @@ export function loadActionOverlay(db) {
             if (resolution)
                 overlay.promotedOpens.set(r.subject_id, resolution);
         }
+        else if (r.kind === "dismiss_decision" && r.subject_type === "decision") {
+            overlay.dismissedDecisions.add(r.subject_id);
+        }
+        else if (r.kind === "revise_decision" && r.subject_type === "decision") {
+            const to = typeof payload?.["to"] === "string" ? payload["to"].trim() : "";
+            if (to)
+                overlay.revisedDecisions.set(r.subject_id, to);
+            else
+                overlay.revisedDecisions.delete(r.subject_id);
+        }
+        else if (r.kind === "merge_entity" && r.subject_type === "entity") {
+            const into = typeof payload?.["into"] === "string" ? payload["into"].trim() : "";
+            if (into)
+                overlay.mergedEntities.set(r.subject_id, into);
+            else
+                overlay.mergedEntities.delete(r.subject_id);
+        }
+        else if (r.kind === "set_coherence" && r.subject_type === "entity") {
+            const state = typeof payload?.["state"] === "string" ? payload["state"] : "";
+            if (state === "active" || state === "sparse" || state === "stale") {
+                overlay.coherenceOverrides.set(r.subject_id, state);
+            }
+            else {
+                // Empty payload reverts to the computed bucket.
+                overlay.coherenceOverrides.delete(r.subject_id);
+            }
+        }
     }
     return overlay;
 }
@@ -82,6 +129,15 @@ export function loadActionOverlay(db) {
 export function openQuestionId(sessionId, text) {
     return `${sessionId}::${stableHash12(text)}`;
 }
+/**
+ * Stable id for a decision: `${sessionId}::dec::${hash12(text)}`. Same
+ * deterministic-hash trick as open questions; the `dec::` infix keeps the
+ * two ID spaces disjoint so a decision and an open question with the same
+ * text in the same session don't collide.
+ */
+export function decisionId(sessionId, text) {
+    return `${sessionId}::dec::${stableHash12(text)}`;
+}
 function stableHash12(text) {
     let h = 0xcbf29ce484222325n;
     for (let i = 0; i < text.length; i++) {

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@@ -1 +1 @@
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+{"version":3,"file":"overlay.js","sourceRoot":"","sources":["../../../src/core/actions/overlay.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAsCH,MAAM,CAAC,MAAM,aAAa,GAAkB;IAC1C,eAAe,EAAE,IAAI,GAAG,EAAE;IAC1B,aAAa,EAAE,IAAI,GAAG,EAAE;IACxB,eAAe,EAAE,IAAI,GAAG,EAAE;IAC1B,eAAe,EAAE,IAAI,GAAG,EAAE;IAC1B,eAAe,EAAE,IAAI,GAAG,EAAE;IAC1B,eAAe,EAAE,IAAI,GAAG,EAAE;IAC1B,aAAa,EAAE,IAAI,GAAG,EAAE;IACxB,aAAa,EAAE,IAAI,GAAG,EAAE;IACxB,kBAAkB,EAAE,IAAI,GAAG,EAAE;IAC7B,gBAAgB,EAAE,IAAI,GAAG,EAAE;IAC3B,kBAAkB,EAAE,IAAI,GAAG,EAAE;IAC7B,cAAc,EAAE,IAAI,GAAG,EAAE;CAC1B,CAAC;AAEF,MAAM,UAAU,iBAAiB,CAAC,EAAqB;IACrD,MAAM,UAAU,GAAG,EAAE;SAClB,OAAO,CAAuB,sEAAsE,CAAC;SACrG,GAAG,EAAE,CAAC;IACT,IAAI,CAAC,UAAU;QAAE,OAAO,aAAa,CAAC;IAEtC,MAAM,OAAO,GAAkB;QAC7B,eAAe,EAAE,IAAI,GAAG,EAAE;QAC1B,aAAa,EAAE,IAAI,GAAG,EAAE;QACxB,eAAe,EAAE,IAAI,GAAG,EAAE;QAC1B,eAAe,EAAE,IAAI,GAAG,EAAE;QAC1B,eAAe,EAAE,IAAI,GAAG,EAAE;QAC1B,eAAe,EAAE,IAAI,GAAG,EAAE;QAC1B,aAAa,EAAE,IAAI,GAAG,EAAE;QACxB,aAAa,EAAE,IAAI,GAAG,EAAE;QACxB,kBAAkB,EAAE,IAAI,GAAG,EAAE;QAC7B,gBAAgB,EAAE,IAAI,GAAG,EAAE;QAC3B,kBAAkB,EAAE,IAAI,GAAG,EAAE;QAC7B,cAAc,EAAE,IAAI,GAAG,EAAE;KAC1B,CAAC;IAEF,0EAA0E;IAC1E,4DAA4D;IAC5D,MAAM,IAAI,GAAG,EAAE;SACZ,OAAO,CAAgB;;;;;KAKvB,CAAC;SACD,GAAG,EAAE,CAAC;IAET,MAAM,GAAG,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACrC,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;QACrB,MAAM,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAE,SAAS,CAAC,CAAC,CAAC,OAAO,CAAoC,CAAC,CAAC,CAAC,IAAI,CAAC;QAC5F,IAAI,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,CAAC,CAAC,YAAY,KAAK,OAAO,EAAE,CAAC;YACvD,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QAC5C,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,QAAQ,IAAI,CAAC,CAAC,YAAY,KAAK,OAAO,EAAE,CAAC;YAC7D,MAAM,KAAK,GAAG,OAAO,OAAO,EAAE,CAAC,eAAe,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7F,IAAI,KAAK,GAAG,GAAG;gBAAE,OAAO,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,KAAK,CAAC,CAAC;QAClE,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,eAAe,IAAI,CAAC,CAAC,YAAY,KAAK,QAAQ,EAAE,CAAC;YACrE,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QAC5C,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,QAAQ,IAAI,CAAC,CAAC,YAAY,KAAK,QAAQ,EAAE,CAAC;YAC9D,MAAM,KAAK,GAAG,OAAO,OAAO,EAAE,CAAC,eAAe,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7F,IAAI,KAAK,GAAG,GAAG;gBAAE,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,KAAK,CAAC,CAAC;QACpE,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,cAAc,IAAI,CAAC,CAAC,YAAY,KAAK,QAAQ,EAAE,CAAC;YACpE,MAAM,OAAO,GAAG,OAAO,OAAO,EAAE,CAAC,UAAU,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;YACvF,IAAI,OAAO;gBAAE,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;QAClE,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,eAAe,IAAI,CAAC,CAAC,YAAY,KAAK,QAAQ,EAAE,CAAC;YACrE,MAAM,EAAE,GAAG,OAAO,OAAO,EAAE,CAAC,IAAI,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC3E,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC,UAAU;gBAAE,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;;gBACxE,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QACpD,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,cAAc,IAAI,CAAC,CAAC,YAAY,KAAK,eAAe,EAAE,CAAC;YAC3E,OAAO,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QAC1C,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,cAAc,IAAI,CAAC,CAAC,YAAY,KAAK,eAAe,EAAE,CAAC;YAC3E,MAAM,UAAU,GAAG,OAAO,OAAO,EAAE,CAAC,YAAY,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACnG,IAAI,UAAU;gBAAE,OAAO,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;QACtE,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,kBAAkB,IAAI,CAAC,CAAC,YAAY,KAAK,UAAU,EAAE,CAAC;YAC1E,OAAO,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QAC/C,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,iBAAiB,IAAI,CAAC,CAAC,YAAY,KAAK,UAAU,EAAE,CAAC;YACzE,MAAM,EAAE,GAAG,OAAO,OAAO,EAAE,CAAC,IAAI,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC3E,IAAI,EAAE;gBAAE,OAAO,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;;gBAClD,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QACrD,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,cAAc,IAAI,CAAC,CAAC,YAAY,KAAK,QAAQ,EAAE,CAAC;YACpE,MAAM,IAAI,GAAG,OAAO,OAAO,EAAE,CAAC,MAAM,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACjF,IAAI,IAAI;gBAAE,OAAO,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC;;gBACpD,OAAO,CAAC,cAAc,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QACnD,CAAC;aAAM,IAAI,CAAC,CAAC,IAAI,KAAK,eAAe,IAAI,CAAC,CAAC,YAAY,KAAK,QAAQ,EAAE,CAAC;YACrE,MAAM,KAAK,GAAG,OAAO,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7E,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,OAAO,EAAE,CAAC;gBAClE,OAAO,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,EAAE,KAAK,CAAC,CAAC;YACtD,CAAC;iBAAM,CAAC;gBACN,gDAAgD;gBAChD,OAAO,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;YAClD,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,cAAc,CAAC,SAAiB,EAAE,IAAY;IAC5D,OAAO,GAAG,SAAS,KAAK,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC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package/dist/core/dataset/build-dataset.d.ts

@@ -17,6 +17,9 @@ export interface DatasetSession {
     readonly summary: string;
     readonly entities: ReadonlyArray<string>;
     readonly decisions: ReadonlyArray<string>;
+    /** Stable ids parallel to `decisions[]`. Same length and order; use to
+     *  target overlay actions (dismiss_decision, revise_decision). */
+    readonly decision_ids: ReadonlyArray<string>;
     readonly open: ReadonlyArray<string>;
     readonly open_questions: ReadonlyArray<{
         id: string;
@@ -29,12 +32,20 @@ export interface DatasetSession {
     readonly supersedes?: string;
     readonly superseded_by?: string;
 }
+export type TopicCoherence = "active" | "sparse" | "stale";
 export interface DatasetEntity {
     readonly canonical: string;
     readonly type: string;
     readonly status: string;
     readonly session_count: number;
     readonly last_seen_session: string | null;
+    /** Renamed display label from the action overlay; absent if not renamed. */
+    readonly display?: string;
+    /** Effective coherence bucket (override if user set one, else computed). */
+    readonly coherence: TopicCoherence;
+    /** Computed bucket from session_count + age, ignoring any override. Lets
+     *  the UI show "would naturally be X" alongside the user assertion. */
+    readonly coherence_computed: TopicCoherence;
 }
 export interface DatasetResponse {
     readonly meta: {
@@ -49,6 +60,8 @@ export interface DatasetResponse {
     readonly entity_colors: Record<string, string>;
     readonly entity_type: Record<string, string>;
     readonly entity_status: Record<string, string>;
+    /** canonical → display label; only canonicals with an active rename appear. */
+    readonly entity_display: Record<string, string>;
     readonly metrics: {
         readonly this_week: number;
         readonly last_week: number;
@@ -61,7 +74,7 @@ export interface DatasetResponse {
     readonly alerts: ReadonlyArray<{
         readonly id: string;
         readonly type: "stale";
-        readonly severity: "high" | "medium";
+        readonly severity: "high" | "medium" | "low";
         readonly entity: string;
         readonly summary: string;
         readonly sessions: ReadonlyArray<string>;

package/dist/core/dataset/build-dataset.js

@@ -11,7 +11,7 @@ import { existsSync } from "node:fs";
 import Database from "better-sqlite3";
 import * as sqliteVec from "sqlite-vec";
 import { liveSessionStatus } from "../storage/live-status.js";
-import { loadActionOverlay, openQuestionId } from "../actions/overlay.js";
+import { loadActionOverlay, openQuestionId, decisionId } from "../actions/overlay.js";
 const EMPTY_DATASET = (dbPath, present) => ({
     meta: {
         last_sync: new Date().toISOString(),
@@ -25,6 +25,7 @@ const EMPTY_DATASET = (dbPath, present) => ({
     entity_colors: {},
     entity_type: {},
     entity_status: {},
+    entity_display: {},
     metrics: { this_week: 0, last_week: 0, sparkline: [0, 0, 0, 0, 0, 0, 0], healthy: 0, sparse: 0, stale: 0, closed_decisions: 0 },
     alerts: [],
     runtimes: [],
@@ -130,14 +131,32 @@ function projectFromDb(db, dbPath, includePaths) {
     `)
         .all();
     const overlay = loadActionOverlay(db);
+    // Count-folding pass (Option B): runs before coherence computation so the
+    // target entity's bucket reflects the absorbed session count.
+    if (overlay.mergedEntities.size > 0) {
+        const byCanonical = new Map(allEntityRows.map((e) => [e.canonical, e]));
+        for (const [source, into] of overlay.mergedEntities) {
+            const src = byCanonical.get(source);
+            const tgt = byCanonical.get(into);
+            if (src && tgt)
+                tgt.session_count += src.session_count;
+        }
+    }
+    const sessionStartByIdForCoherence = new Map(sessionRows.map((s) => [s.id, s.started_at]));
+    const nowMs = Date.now();
     for (const e of allEntityRows) {
-        if (overlay.retiredEntities.has(e.canonical))
+        if (overlay.retiredEntities.has(e.canonical) || overlay.mergedEntities.has(e.canonical))
             e.status = "retired";
         else if (overlay.snoozedEntities.has(e.canonical))
             e.status = "snoozed";
         const newType = overlay.labeledEntities.get(e.canonical);
         if (newType)
             e.type = newType;
+        const newDisplay = overlay.renamedEntities.get(e.canonical);
+        if (newDisplay)
+            e.display = newDisplay;
+        e.coherence_computed = computeCoherence(e, sessionStartByIdForCoherence, nowMs);
+        e.coherence = overlay.coherenceOverrides.get(e.canonical) ?? e.coherence_computed;
     }
     const entityRows = includePaths
         ? allEntityRows
@@ -153,6 +172,24 @@ function projectFromDb(db, dbPath, includePaths) {
         const promotedDecisions = rawOpen
             .filter((o) => overlay.promotedOpens.has(o.id))
             .map((o) => overlay.promotedOpens.get(o.id));
+        // Project decision overlays: dismissed lines drop out; revised lines
+        // show the corrected text. Promoted-from-open lines pass through as-is
+        // (the open-question id already governs them).
+        const rawDecisions = decisionsBySession.get(s.id) ?? [];
+        const projectedDecisions = [];
+        const projectedDecisionIds = [];
+        for (const text of rawDecisions) {
+            const id = decisionId(s.id, text);
+            if (overlay.dismissedDecisions.has(id))
+                continue;
+            const revised = overlay.revisedDecisions.get(id);
+            projectedDecisions.push(revised ?? text);
+            projectedDecisionIds.push(id);
+        }
+        for (const text of promotedDecisions) {
+            projectedDecisions.push(text);
+            projectedDecisionIds.push(decisionId(s.id, text));
+        }
         return {
             id: s.id,
             date: (s.started_at ?? "").slice(0, 10),
@@ -161,7 +198,8 @@ function projectFromDb(db, dbPath, includePaths) {
             label: s.label,
             summary: s.summary,
             entities: includePaths ? rawEntities : rawEntities.filter((name) => keptEntities.has(name)),
-            decisions: [...(decisionsBySession.get(s.id) ?? []), ...promotedDecisions],
+            decisions: projectedDecisions,
+            decision_ids: projectedDecisionIds,
             open: activeOpen.map((o) => o.text),
             open_questions: activeOpen.map((o) => ({ id: o.id, text: o.text, resolved: false })),
             status,
@@ -176,10 +214,13 @@ function projectFromDb(db, dbPath, includePaths) {
     const entityColors = {};
     const entityType = {};
     const entityStatus = {};
+    const entityDisplay = {};
     for (const e of entityRows) {
         entityColors[e.canonical] = stableColor(e.canonical);
         entityType[e.canonical] = e.type;
         entityStatus[e.canonical] = e.status;
+        if (e.display)
+            entityDisplay[e.canonical] = e.display;
     }
     const metrics = computeMetrics(sessions, entityRows);
     const alerts = computeStaleAlerts(sessions, entityRows, overlay);
@@ -197,6 +238,7 @@ function projectFromDb(db, dbPath, includePaths) {
         entity_colors: entityColors,
         entity_type: entityType,
         entity_status: entityStatus,
+        entity_display: entityDisplay,
         metrics,
         alerts,
         runtimes,
@@ -263,19 +305,18 @@ function computeMetrics(sessions, entityRows) {
             lastWeek += 1;
         }
     }
-    const sessionsById = new Map(sessions.map((s) => [s.id, s]));
+    // Aggregate by the effective coherence (override wins, else computed) so
+    // the headline bars match what the user sees after asserting a bucket.
     let healthy = 0;
     let sparse = 0;
     let stale = 0;
     for (const e of entityRows) {
         if (e.session_count === 0)
             continue;
-        const last = sessionsById.get(e.last_seen_session ?? "");
-        const lastT = last?.started_at ? Date.parse(last.started_at) : NaN;
-        const ageDays = Number.isFinite(lastT) ? (now - lastT) / 86_400_000 : 999;
-        if (ageDays > 30)
+        const bucket = e.coherence ?? "sparse";
+        if (bucket === "stale")
             stale += 1;
-        else if (e.session_count >= 3)
+        else if (bucket === "active")
             healthy += 1;
         else
             sparse += 1;
@@ -283,6 +324,20 @@ function computeMetrics(sessions, entityRows) {
     const closedDecisions = sessions.reduce((sum, s) => sum + (s.status === "superseded" ? 0 : s.decisions.length), 0);
     return { this_week: thisWeek, last_week: lastWeek, sparkline, healthy, sparse, stale, closed_decisions: closedDecisions };
 }
+/** Natural coherence bucket for an entity, ignoring overlay overrides.
+ *  Stale dominates: any topic last touched >30d is stale regardless of count. */
+function computeCoherence(e, startedAtBySession, nowMs) {
+    if (e.session_count === 0)
+        return "sparse";
+    const startedAt = startedAtBySession.get(e.last_seen_session ?? "") ?? null;
+    const lastT = startedAt ? Date.parse(startedAt) : NaN;
+    const ageDays = Number.isFinite(lastT) ? (nowMs - lastT) / 86_400_000 : 999;
+    if (ageDays > 30)
+        return "stale";
+    if (e.session_count >= 3)
+        return "active";
+    return "sparse";
+}
 function computeStaleAlerts(sessions, entityRows, overlay) {
     const now = Date.now();
     const sessionsById = new Map(sessions.map((s) => [s.id, s]));
@@ -313,7 +368,7 @@ function computeStaleAlerts(sessions, entityRows, overlay) {
         alerts.push({
             id: alertId,
             type: "stale",
-            severity: ageDays > 60 ? "high" : "medium",
+            severity: ageDays > 60 ? "high" : ageDays > 45 ? "medium" : "low",
             entity: e.canonical,
             summary,
             sessions: last ? [last.id] : [],
@@ -321,7 +376,9 @@ function computeStaleAlerts(sessions, entityRows, overlay) {
             last_touch_at: last?.started_at ?? null,
         });
     }
-    alerts.sort((a, b) => (a.severity === "high" ? 0 : 1) - (b.severity === "high" ? 0 : 1));
+    // high → medium → low, then secondary by age desc so older items surface first within a tier.
+    const severityRank = { high: 0, medium: 1, low: 2 };
+    alerts.sort((a, b) => severityRank[a.severity] - severityRank[b.severity] || b.age_days - a.age_days);
     return alerts;
 }
 const HUES = [200, 270, 320, 30, 90, 150, 220, 290, 340, 50, 110, 170];

package/dist/core/dataset/build-dataset.js.map

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package/dist/core/hook/miss-detect.d.ts

@@ -0,0 +1,32 @@
+/**
+ * Detect "recall misses" — sessions the agent explicitly fetched or cited
+ * in its response but which the hook's pre-prompt recall never surfaced
+ * in this conversation.
+ *
+ * A miss is the inverse signal of a citation:
+ *  - Citation = surfaced id appeared in the agent's tool calls / prose
+ *  - Miss     = id appeared in a get_session(id) or cite_session(id) call
+ *               but was NOT surfaced
+ *
+ * Only explicit-id tool_use calls count. We don't scan recall_sessions
+ * results — those are exploratory and don't mean the agent thought any
+ * specific returned id was the right answer. get_session and cite_session,
+ * by contrast, are deterministic single-id signals: "I want this session
+ * specifically" or "I am citing this exact session."
+ *
+ * Aggregated miss data shows where the hook's selection gate is wrong —
+ * sessions that were relevant but didn't score high enough to fire. Spec E
+ * v1 is passive: just log, surface via the `nlm misses` CLI for review.
+ * Future specs may consume this data to retrain reranking or trigger
+ * targeted reclassification.
+ */
+import type { ToolUseBlock } from "./transcript.js";
+export interface DetectedMiss {
+    readonly id: string;
+    readonly kind: "get_session" | "cite_session";
+}
+export interface MissDetectInput {
+    readonly toolUses: ReadonlyArray<ToolUseBlock>;
+    readonly surfacedIds: Iterable<string>;
+}
+export declare function detectMisses(input: MissDetectInput): DetectedMiss[];

package/dist/core/hook/miss-detect.js

@@ -0,0 +1,67 @@
+/**
+ * Detect "recall misses" — sessions the agent explicitly fetched or cited
+ * in its response but which the hook's pre-prompt recall never surfaced
+ * in this conversation.
+ *
+ * A miss is the inverse signal of a citation:
+ *  - Citation = surfaced id appeared in the agent's tool calls / prose
+ *  - Miss     = id appeared in a get_session(id) or cite_session(id) call
+ *               but was NOT surfaced
+ *
+ * Only explicit-id tool_use calls count. We don't scan recall_sessions
+ * results — those are exploratory and don't mean the agent thought any
+ * specific returned id was the right answer. get_session and cite_session,
+ * by contrast, are deterministic single-id signals: "I want this session
+ * specifically" or "I am citing this exact session."
+ *
+ * Aggregated miss data shows where the hook's selection gate is wrong —
+ * sessions that were relevant but didn't score high enough to fire. Spec E
+ * v1 is passive: just log, surface via the `nlm misses` CLI for review.
+ * Future specs may consume this data to retrain reranking or trigger
+ * targeted reclassification.
+ */
+const MIN_ID_LEN = 6;
+export function detectMisses(input) {
+    const surfaced = new Set();
+    for (const id of input.surfacedIds) {
+        if (id.length >= MIN_ID_LEN)
+            surfaced.add(id);
+    }
+    const seenMissed = new Set();
+    const misses = [];
+    for (const tu of input.toolUses) {
+        if (!isNlmTool(tu.name))
+            continue;
+        const kind = explicitIdKind(tu.name);
+        if (!kind)
+            continue;
+        const id = extractId(tu.input);
+        if (!id || id.length < MIN_ID_LEN)
+            continue;
+        if (surfaced.has(id))
+            continue;
+        if (seenMissed.has(id))
+            continue;
+        seenMissed.add(id);
+        misses.push({ id, kind });
+    }
+    return misses;
+}
+function isNlmTool(name) {
+    return /^mcp__[^_]*nlm[^_]*__/.test(name);
+}
+function explicitIdKind(name) {
+    if (name.endsWith("__get_session"))
+        return "get_session";
+    if (name.endsWith("__cite_session"))
+        return "cite_session";
+    return null;
+}
+function extractId(input) {
+    if (input === null || typeof input !== "object")
+        return null;
+    const obj = input;
+    const candidate = obj["id"];
+    return typeof candidate === "string" ? candidate : null;
+}
+//# sourceMappingURL=miss-detect.js.map

package/dist/core/hook/miss-detect.js.map

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