@isaacriehm/cairn-core 0.21.0 → 0.22.1

package/dist/mcp/schemas.js

@@ -31,6 +31,28 @@ export const componentGetInput = {
     /** Optional workspace filter (monorepo). Omit for single-app. */
     workspace: z.string().optional(),
 };
+export const componentRegisterInput = {
+    /** Repo-relative POSIX path of the component file. */
+    file: z.string().min(1),
+    /** The export symbol being registered — the natural key + identity. */
+    export_name: z.string().min(1),
+    /** The `@cairn <Name>` value (usually === export_name). */
+    name: z.string().min(1),
+    category: z.string().min(1),
+    purpose: z.string().min(1),
+    aliases: z.array(z.string()).default([]),
+    /** Owning workspace; omit / "" for single-app. */
+    workspace: z.string().optional(),
+    singleton: z.boolean().optional(),
+    status: z.string().optional(),
+    uses: z.array(z.string()).optional(),
+};
+export const componentReconfirmInput = {
+    /** Reconfirm a single file's component; omit to sweep every flagged unit. */
+    file: z.string().min(1).optional(),
+    /** Hard cap on fresh Haiku calls this run; the rest stay flagged (deferred). */
+    cap: z.number().int().positive().max(50).optional(),
+};
 // ── Read tools — 3-layer progressive retrieval ─────────────────────────────
 export const searchInput = {
     query: z.string().min(1),
@@ -189,6 +211,10 @@ export const retireInvariantInput = {
     id: z.string().regex(/^INV-[0-9a-f]{7,}$/, "id must match INV-<hash7>"),
     reason: z.string().min(1).optional(),
 };
+export const migrateInput = {
+    /** Preview the pending review migrations without writing anything. */
+    dry_run: z.boolean().optional(),
+};
 export const resolveAttentionInput = {
     /**
      * Item id from the attention skill — DEC-<hash> for a draft, the

package/dist/mcp/schemas.js.map

@@ -1 +1 @@
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package/dist/mcp/server.js

@@ -1,5 +1,4 @@
 import { existsSync } from "node:fs";
-import { join } from "node:path";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { logger } from "../logger.js";
@@ -8,6 +7,7 @@ import { isMcpError, mcpError } from "./errors.js";
 import { asMcpResult } from "./result.js";
 import { recordCall } from "./telemetry.js";
 import { allTools } from "./tools/index.js";
+import { cairnDir } from "@isaacriehm/cairn-state";
 const log = logger("mcp.server");
 export async function startMcpServer(opts) {
     const { ctx } = opts;
@@ -15,8 +15,8 @@ export async function startMcpServer(opts) {
     // Finding 2: Unload init tools post-adoption to save context window.
     // Adoption is "complete" if config.yaml exists but init-state.json
     // (the v0.3.5 state machine sentinel) is gone.
-    const isAdopted = existsSync(join(ctx.repoRoot, ".cairn", "config.yaml")) &&
-        !existsSync(join(ctx.repoRoot, ".cairn", "init-state.json"));
+    const isAdopted = existsSync(cairnDir(ctx.repoRoot, "config.yaml")) &&
+        !existsSync(cairnDir(ctx.repoRoot, "init-state.json"));
     for (const tool of allTools) {
         if (isAdopted && tool.name.startsWith("cairn_init_")) {
             continue;

package/dist/mcp/server.js.map

@@ -1 +1 @@
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package/dist/mcp/telemetry.js

@@ -1,10 +1,11 @@
 import { appendFileSync, existsSync, mkdirSync } from "node:fs";
-import { dirname, join } from "node:path";
+import { dirname } from "node:path";
 import { appendTrace } from "../trace/index.js";
+import { cairnDir } from "@isaacriehm/cairn-state";
 export function recordCall(ctx, row) {
     const path = ctx.runId !== undefined
-        ? join(ctx.repoRoot, ".cairn", "runs", "active", ctx.runId, "mcp-calls.jsonl")
-        : join(ctx.repoRoot, ".cairn", "staleness", "mcp-calls.jsonl");
+        ? cairnDir(ctx.repoRoot, "runs", "active", ctx.runId, "mcp-calls.jsonl")
+        : cairnDir(ctx.repoRoot, "staleness", "mcp-calls.jsonl");
     const dir = dirname(path);
     if (!existsSync(dir)) {
         mkdirSync(dir, { recursive: true });

package/dist/mcp/telemetry.js.map

@@ -1 +1 @@
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+{"version":3,"file":"telemetry.js","sourceRoot":"","sources":["../../src/mcp/telemetry.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,SAAS,CAAC;AAChE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAEhD,OAAO,EAAE,QAAQ,EAAE,MAAM,yBAAyB,CAAC;AAsBnD,MAAM,UAAU,UAAU,CAAC,GAAe,EAAE,GAAiB;IAC3D,MAAM,IAAI,GACR,GAAG,CAAC,KAAK,KAAK,SAAS;QACrB,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,KAAK,EAAE,iBAAiB,CAAC;QACxE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,QAAQ,EAAE,WAAW,EAAE,iBAAiB,CAAC,CAAC;IAC7D,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAC1B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACrB,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IACtC,CAAC;IACD,cAAc,CAAC,IAAI,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IAEzD,WAAW,CAAC;QACV,EAAE,EAAE,GAAG,CAAC,EAAE;QACV,MAAM,EAAE,KAAK;QACb,IAAI,EAAE,GAAG,CAAC,IAAI;QACd,SAAS,EAAE,GAAG,CAAC,QAAQ;QACvB,UAAU,EAAE,IAAI;QAChB,WAAW,EAAE,GAAG,CAAC,WAAW;QAC5B,EAAE,EAAE,GAAG,CAAC,WAAW,KAAK,IAAI;QAC5B,OAAO,EAAE;YACP,IAAI,EAAE,GAAG,CAAC,IAAI;YACd,WAAW,EAAE,GAAG,CAAC,WAAW;YAC5B,GAAG,CAAC,GAAG,CAAC,cAAc,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,cAAc,EAAE,GAAG,CAAC,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACnF,GAAG,CAAC,GAAG,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,GAAG,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SAC1D;KACF,CAAC,CAAC;AACL,CAAC"}

package/dist/mcp/tools/component-reconfirm.d.ts

@@ -0,0 +1,7 @@
+import type { ToolDef } from "./types.js";
+interface Input {
+    file?: string;
+    cap?: number;
+}
+export declare const componentReconfirmTool: ToolDef<Input>;
+export {};

package/dist/mcp/tools/component-reconfirm.js

@@ -0,0 +1,39 @@
+import { isGhost } from "@isaacriehm/cairn-state";
+import { runComponentReconfirm } from "../../components/reconfirm.js";
+import { mcpError } from "../errors.js";
+import { componentReconfirmInput } from "../schemas.js";
+/**
+ * Re-confirm headerless components the freshness gate flagged as
+ * identity-changed (§3.8.1). Ghost-only. Runs the narrow **Haiku** yes/no
+ * judge ("does the stored category/purpose still fit?") over flagged entries —
+ * "fits" clears the flag, "stale" leaves it for the operator to re-register.
+ * Verdicts are cached on the body fingerprint and the run is hard-capped, so a
+ * sweep can't runaway-burn quota. This is the deferred, quota-expected reclassify
+ * pass — never the hot edit path. Committed projects have no headerless registry,
+ * so the tool refuses there.
+ */
+async function handler(ctx, input) {
+    if (!isGhost(ctx.repoRoot)) {
+        return mcpError("NOT_ALLOWED", "cairn_component_reconfirm is the ghost-mode reclassify pass. Committed projects carry no headerless registry — re-confirm a component by editing its in-file `@cairn` header instead.");
+    }
+    const res = await runComponentReconfirm({
+        repoRoot: ctx.repoRoot,
+        ...(input.file !== undefined ? { onlyFile: input.file } : {}),
+        ...(input.cap !== undefined ? { cap: input.cap } : {}),
+    });
+    return {
+        considered: res.considered,
+        cleared: res.cleared,
+        still_flagged: res.stillStale + res.deferred,
+        deferred: res.deferred,
+        haiku_calls: res.haikuCalls,
+        cache_hits: res.cacheHits,
+    };
+}
+export const componentReconfirmTool = {
+    name: "cairn_component_reconfirm",
+    description: "Ghost mode only. Re-confirm components the freshness gate flagged as identity-changed: a narrow Haiku judge decides whether each one's stored category/purpose still fits its current code. 'fits' clears the flag; 'stale' leaves it for you to re-register via cairn_component_register. Pass `file` to reconfirm one unit, or omit to sweep all flagged. `cap` bounds Haiku calls per run (rest deferred). Verdicts cache on the body fingerprint. Refuses in committed mode.",
+    inputSchema: componentReconfirmInput,
+    handler,
+};
+//# sourceMappingURL=component-reconfirm.js.map

package/dist/mcp/tools/component-reconfirm.js.map

@@ -0,0 +1 @@
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package/dist/mcp/tools/component-register.d.ts

@@ -0,0 +1,15 @@
+import type { ToolDef } from "./types.js";
+interface Input {
+    file: string;
+    export_name: string;
+    name: string;
+    category: string;
+    purpose: string;
+    aliases: string[];
+    workspace?: string;
+    singleton?: boolean;
+    status?: string;
+    uses?: string[];
+}
+export declare const componentRegisterTool: ToolDef<Input>;
+export {};

package/dist/mcp/tools/component-register.js

@@ -0,0 +1,65 @@
+import { existsSync, readFileSync } from "node:fs";
+import { join } from "node:path";
+import { bodyContentHash, extractExportNames, isGhost, profileForFile, registerComponentEntry, } from "@isaacriehm/cairn-state";
+import { mcpError } from "../errors.js";
+import { componentRegisterInput } from "../schemas.js";
+/**
+ * Register one component into the out-of-repo headerless registry (§3.8.1).
+ * This is the ghost write path that replaces the `@cairn` annotator's source
+ * `Edit` — the classification lands in `cairnHome/ground/components/
+ * registry.yaml`, keyed (workspace, file, export), and the client source file
+ * is never touched. Committed projects register via the in-file header, so the
+ * tool refuses there to keep the one-SoT-per-mode rule clean.
+ */
+async function handler(ctx, input) {
+    if (!isGhost(ctx.repoRoot)) {
+        return mcpError("NOT_ALLOWED", "cairn_component_register is the ghost-mode write path. Committed projects register a component by its in-file `@cairn <Name>` header (add the header / run the annotator), not via this tool.");
+    }
+    const abs = join(ctx.repoRoot, input.file);
+    if (!existsSync(abs)) {
+        return mcpError("FILE_NOT_FOUND", `${input.file} does not exist under the repo root — register an existing component file.`);
+    }
+    let source;
+    try {
+        source = readFileSync(abs, "utf8");
+    }
+    catch (err) {
+        return mcpError("INTERNAL_ERROR", `could not read ${input.file}: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    const entry = {
+        workspace: input.workspace ?? "",
+        file: input.file,
+        export: input.export_name,
+        name: input.name,
+        category: input.category,
+        purpose: input.purpose,
+        aliases: input.aliases,
+        uses: input.uses ?? [],
+        // v1 fingerprint: whole-file body hash (one component per file is the UI
+        // convention, so the file body is the component span). The export-span hash
+        // is a later precision refinement.
+        anchor: { content_hash: bodyContentHash(source) },
+        // Identity snapshot — the freshness gate (§3.8.1) compares the file's
+        // future exports/shape against these to tell an internal refactor from a
+        // genuine identity change without ever calling the LLM.
+        exports: extractExportNames(source, input.file),
+        unit_shaped: profileForFile(input.file)?.isUnitShaped(source, input.file) ?? false,
+        ...(input.singleton !== undefined ? { singleton: input.singleton } : {}),
+        ...(input.status !== undefined ? { status: input.status } : {}),
+    };
+    registerComponentEntry(ctx.repoRoot, entry);
+    return {
+        registered: true,
+        workspace: entry.workspace,
+        file: entry.file,
+        export: entry.export,
+        name: entry.name,
+    };
+}
+export const componentRegisterTool = {
+    name: "cairn_component_register",
+    description: "Ghost mode only. Register a component into the out-of-repo headerless registry so it joins the store WITHOUT writing a `@cairn` header into client source. Pass the file, the export symbol, and the classification (name/category/purpose/aliases). Use this to resolve an `unregistered unit` finding. Committed projects use the in-file header instead and the tool refuses there.",
+    inputSchema: componentRegisterInput,
+    handler,
+};
+//# sourceMappingURL=component-register.js.map

package/dist/mcp/tools/component-register.js.map

@@ -0,0 +1 @@
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package/dist/mcp/tools/index.js

@@ -2,6 +2,8 @@ import { attentionDedupTool } from "./attention-dedup.js";
 import { bootstrapRetryTool } from "./bootstrap-retry.js";
 import { canonicalForTopicTool } from "./canonical-for-topic.js";
 import { componentGetTool } from "./component-get.js";
+import { componentRegisterTool } from "./component-register.js";
+import { componentReconfirmTool } from "./component-reconfirm.js";
 import { componentsInScopeTool } from "./components-in-scope.js";
 import { decisionGetTool } from "./decision-get.js";
 import { inScopeTool } from "./in-scope.js";
@@ -18,6 +20,7 @@ import { missionSetExitGateTool } from "./mission-set-exit-gate.js";
 import { invariantGetTool } from "./invariant-get.js";
 import { recordDecisionTool } from "./record-decision.js";
 import { retireDecisionTool, retireInvariantTool } from "./retire-entity.js";
+import { migrateTool } from "./migrate.js";
 import { resolveAttentionTool } from "./resolve-attention.js";
 import { searchTool } from "./search.js";
 import { resumeTool } from "./resume.js";
@@ -41,6 +44,11 @@ export const allTools = [
     // Write — entity retirement (the OUT path)
     retireDecisionTool,
     retireInvariantTool,
+    // Write — apply pending review-class migrations inline
+    migrateTool,
+    // Write — headerless component registry (ghost §3.8.1)
+    componentRegisterTool,
+    componentReconfirmTool,
     taskCreateTool,
     taskCompleteTool,
     taskReopenTool,

package/dist/mcp/tools/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/mcp/tools/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,qBAAqB,EAAE,MAAM,0BAA0B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAC;AAChE,OAAO,EAAE,sBAAsB,EAAE,MAAM,0BAA0B,CAAC;AAClE,OAAO,EAAE,qBAAqB,EAAE,MAAM,0BAA0B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EACL,cAAc,EACd,WAAW,GACZ,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAC;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAC;AAClD,OAAO,EAAE,oBAAoB,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AACxD,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AACxD,OAAO,EAAE,uBAAuB,EAAE,MAAM,4BAA4B,CAAC;AACrE,OAAO,EAAE,sBAAsB,EAAE,MAAM,4BAA4B,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,kBAAkB,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAC3C,OAAO,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAC9D,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AACzC,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAC;AAClD,OAAO,EAAE,qBAAqB,EAAE,MAAM,0BAA0B,CAAC;AACjE,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAC;AAElD,MAAM,CAAC,MAAM,QAAQ,GAAqB;IACxC,yBAAyB;IACzB,eAAe;IACf,qBAAqB;IACrB,gBAAgB;IAChB,WAAW;IACX,4BAA4B;IAC5B,qBAAqB;IACrB,gBAAgB;IAChB,4BAA4B;IAC5B,UAAU;IACV,QAAQ;IACR,kBAAkB;IAClB,2CAA2C;IAC3C,kBAAkB;IAClB,mBAAmB;IACnB,uDAAuD;IACvD,WAAW;IACX,uDAAuD;IACvD,qBAAqB;IACrB,sBAAsB;IACtB,cAAc;IACd,gBAAgB;IAChB,cAAc;IACd,qBAAqB;IACrB,sBAAsB;IACtB,UAAU;IACV,qCAAqC;IACrC,oBAAoB;IACpB,kBAAkB;IAClB,2EAA2E;IAC3E,kBAAkB;IAClB,yDAAyD;IACzD,cAAc;IACd,WAAW;IACX,oCAAoC;IACpC,gBAAgB;IAChB,sBAAsB;IACtB,cAAc;IACd,oBAAoB;IACpB,kBAAkB;IAClB,iBAAiB;IACjB,iBAAiB;IACjB,uBAAuB;IACvB,sBAAsB;CACvB,CAAC"}

package/dist/mcp/tools/init-phases.d.ts

@@ -42,6 +42,8 @@ interface PhaseRunInput {
     answer?: string;
 }
 interface ResumeToolInput {
+    /** When true, register the repo ghost before resolving the next phase. */
+    ghost?: boolean;
 }
 export declare const initRunTool: ToolDef<PhaseRunInput>;
 export declare const initResumeTool: ToolDef<ResumeToolInput>;

package/dist/mcp/tools/init-phases.js

@@ -35,7 +35,8 @@
  * phase outputs — a single bad call could nuke a 90KB mapper run.
  */
 import { z } from "zod";
-import { PHASE_IDS, clearPhaseState, clearProgress, freshPhaseState, readPhaseState, resumePhases, runPhase1Detect, runPhase2Walker, runPhase3Mapper, runPhase4Seed, runPhase5Preflight, runPhase6Brand, runPhase7TopicIndex, runPhase8DocsIngest, runPhase9aWalker, runPhase9bCurate, runPhase9cEmit, runPhase9dCompWalk, runPhase9eCompAnnotate, runPhase9fCompEmit, runPhase10RulesMerge, runPhase11Baseline, runPhase12Strip, runPhase13Multidev, writePhaseState, writeProgress, } from "../../init/index.js";
+import { registerGhostRepo } from "@isaacriehm/cairn-state";
+import { PHASE_IDS, clearPhaseState, clearProgress, freshPhaseState, readPhaseState, resumePhases, runPhase1Detect, runPhase2Walker, runPhase3Mapper, runPhase4Seed, runPhase5Preflight, runPhase6Brand, runPhase7TopicIndex, runPhase8DocsIngest, runPhase9aWalker, runPhase9bCurate, runPhase9cEmit, runPhase9dCompWalk, runPhase9eCompAnnotate, runPhase9fCompEmit, runPhase10RulesMerge, runPhase11Baseline, runPhase13Multidev, writePhaseState, writeProgress, } from "../../init/index.js";
 import { mcpError } from "../errors.js";
 const phaseIdEnum = z.enum(PHASE_IDS);
 const phaseStateSchema = z.object({
@@ -57,7 +58,16 @@ const phaseRunInput = {
     // into state.answer before invoking the phase runner.
     answer: z.string().optional(),
 };
-const initResumeInput = {};
+const initResumeInput = {
+    // Ghost adoption — register this repo as ghost BEFORE the pipeline writes
+    // its first byte. The cairn-adopt skill passes this on the very first
+    // resume call (after the operator picks `ghost` at the top of adoption) so
+    // the fresh init-state, the Phase 4 seed, and every later writer resolve to
+    // the out-of-repo home. Idempotent on a mid-adoption resume (the registry
+    // entry persists; re-registering rewrites the same record). Mirrors the CLI
+    // `cairn init --ghost` → `RunInitArgs.ghost`. See ghost-mode design
+    ghost: z.boolean().optional(),
+};
 const RUNNERS = {
     "1-detect": runPhase1Detect,
     "2-walker": runPhase2Walker,
@@ -75,7 +85,6 @@ const RUNNERS = {
     "9f-comp-emit": runPhase9fCompEmit,
     "10-rules-merge": runPhase10RulesMerge,
     "11-baseline": runPhase11Baseline,
-    "12-strip": runPhase12Strip,
     "13-multidev": runPhase13Multidev,
 };
 function toSlim(result) {
@@ -169,9 +178,16 @@ function makePhaseRunTool() {
 function makeResumeTool() {
     return {
         name: "cairn_init_resume",
-        description: "Read the on-disk init state for the current repo and return the next phase to invoke. The cairn-adopt skill calls this once at the start of the pipeline (and after any operator interruption) to find where to pick up. Returns { status: 'ready' | 'done', nextPhase: PhaseId | null, repoRoot }. For a fresh start (no `.cairn/init-state.json`), the tool persists a fresh PhaseState to disk so the very next `cairn_init_run` call can read it back without the skill having to thread state through tool arguments.",
+        description: "Read the on-disk init state for the current repo and return the next phase to invoke. The cairn-adopt skill calls this once at the start of the pipeline (and after any operator interruption) to find where to pick up. Returns { status: 'ready' | 'done', nextPhase: PhaseId | null, repoRoot }. For a fresh start (no `.cairn/init-state.json`), the tool persists a fresh PhaseState to disk so the very next `cairn_init_run` call can read it back without the skill having to thread state through tool arguments. Pass `ghost: true` ONLY on the first call of a fresh adoption when the operator chose ghost mode — it registers the repo as ghost before any state is written, so the whole pipeline (state file, Phase 4 seed, git hooks) resolves to the out-of-repo home and nothing Cairn-shaped touches the client tree.",
         inputSchema: initResumeInput,
-        handler: async (ctx) => {
+        handler: async (ctx, input) => {
+            // Ghost registration must precede resumePhases: resume seeds a fresh
+            // PhaseState to disk via `cairnDir`, which only relocates out-of-repo
+            // once the registry entry exists. Register first → fresh state lands
+            // out-of-repo. Idempotent if already ghost-registered.
+            if (input.ghost === true) {
+                registerGhostRepo(ctx.repoRoot);
+            }
             const report = resumePhases(ctx.repoRoot);
             // For a fresh start, ensure state.repoRoot matches ctx.repoRoot
             // (resumePhases uses freshPhaseState(ctx.repoRoot) for this case).

package/dist/mcp/tools/init-phases.js.map

@@ -1 +1 @@
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package/dist/mcp/tools/migrate.d.ts

@@ -0,0 +1,21 @@
+/**
+ * `cairn_migrate` — apply pending `review`-class `.cairn/` migrations inline.
+ *
+ * `safe`-class migrations auto-apply silently on session open. The
+ * `review`-class ones rewrite source / hard-delete state / make a judgement
+ * call, so they wait for a human. Historically that wait was a CLI nudge
+ * ("run `cairn migrate --all`") the operator had to act on out-of-band — the
+ * agent could see the pending list at SessionStart but had no in-session verb
+ * to clear it. This tool IS that verb: the SessionStart migration banner now
+ * points the agent here, so it can explain each pending migration and apply
+ * them in the same turn once the operator says go.
+ *
+ * `dry_run` previews (what would apply / queue, no writes). The default
+ * applies the full set, review included.
+ */
+import type { ToolDef } from "./types.js";
+interface Input {
+    dry_run?: boolean;
+}
+export declare const migrateTool: ToolDef<Input>;
+export {};

package/dist/mcp/tools/migrate.js

@@ -0,0 +1,49 @@
+/**
+ * `cairn_migrate` — apply pending `review`-class `.cairn/` migrations inline.
+ *
+ * `safe`-class migrations auto-apply silently on session open. The
+ * `review`-class ones rewrite source / hard-delete state / make a judgement
+ * call, so they wait for a human. Historically that wait was a CLI nudge
+ * ("run `cairn migrate --all`") the operator had to act on out-of-band — the
+ * agent could see the pending list at SessionStart but had no in-session verb
+ * to clear it. This tool IS that verb: the SessionStart migration banner now
+ * points the agent here, so it can explain each pending migration and apply
+ * them in the same turn once the operator says go.
+ *
+ * `dry_run` previews (what would apply / queue, no writes). The default
+ * applies the full set, review included.
+ */
+import { runMigrations } from "../../migrate/index.js";
+import { requireBootstrap } from "../bootstrap-guard.js";
+import { migrateInput } from "../schemas.js";
+export const migrateTool = {
+    name: "cairn_migrate",
+    description: "Apply pending review-class `.cairn/` migrations — the ones the SessionStart 'Cairn — migrations' banner flagged as needing confirmation. These rewrite or hard-delete committed state (e.g. dropping dead init scaffolding, untracking committed derived state), so summarize what each does and get the operator's OK before calling. Pass dry_run:true to preview without writing. Safe-class migrations already auto-applied on session open — this is only for the review-class queue.",
+    inputSchema: migrateInput,
+    handler: async (ctx, input) => {
+        const block = requireBootstrap(ctx.repoRoot);
+        if (block !== null)
+            return block;
+        const dryRun = input.dry_run === true;
+        const result = await runMigrations({
+            repoRoot: ctx.repoRoot,
+            includeReview: true,
+            dryRun,
+        });
+        return {
+            ok: true,
+            dry_run: dryRun,
+            pin: result.pin,
+            new_pin: result.newPin,
+            current: result.current,
+            applied: result.outcomes
+                .filter((o) => o.status === "applied" || o.status === "would-apply")
+                .map((o) => ({ id: o.id, class: o.class, status: o.status, detail: o.detail })),
+            still_pending: result.pendingReview,
+            note: result.ran === false
+                ? "another process holds the migrate lock — nothing applied this call"
+                : undefined,
+        };
+    },
+};
+//# sourceMappingURL=migrate.js.map

package/dist/mcp/tools/migrate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"migrate.js","sourceRoot":"","sources":["../../../src/mcp/tools/migrate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAEvD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAO7C,MAAM,CAAC,MAAM,WAAW,GAAmB;IACzC,IAAI,EAAE,eAAe;IACrB,WAAW,EACT,4dAA4d;IAC9d,WAAW,EAAE,YAAY;IACzB,OAAO,EAAE,KAAK,EAAE,GAAe,EAAE,KAAY,EAAoB,EAAE;QACjE,MAAM,KAAK,GAAG,gBAAgB,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC7C,IAAI,KAAK,KAAK,IAAI;YAAE,OAAO,KAAK,CAAC;QACjC,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,KAAK,IAAI,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,aAAa,CAAC;YACjC,QAAQ,EAAE,GAAG,CAAC,QAAQ;YACtB,aAAa,EAAE,IAAI;YACnB,MAAM;SACP,CAAC,CAAC;QACH,OAAO;YACL,EAAE,EAAE,IAAI;YACR,OAAO,EAAE,MAAM;YACf,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,OAAO,EAAE,MAAM,CAAC,MAAM;YACtB,OAAO,EAAE,MAAM,CAAC,OAAO;YACvB,OAAO,EAAE,MAAM,CAAC,QAAQ;iBACrB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,SAAS,IAAI,CAAC,CAAC,MAAM,KAAK,aAAa,CAAC;iBACnE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACjF,aAAa,EAAE,MAAM,CAAC,aAAa;YACnC,IAAI,EACF,MAAM,CAAC,GAAG,KAAK,KAAK;gBAClB,CAAC,CAAC,oEAAoE;gBACtE,CAAC,CAAC,SAAS;SAChB,CAAC;IACJ,CAAC;CACF,CAAC"}

package/dist/mcp/tools/mission-advance.js

@@ -1,6 +1,6 @@
 import { existsSync, mkdirSync, readFileSync, unlinkSync, writeFileSync, } from "node:fs";
-import { dirname, join } from "node:path";
-import { appendMissionJournal, findActiveMission, readMissionState, readRoadmap, writeMissionState, } from "@isaacriehm/cairn-state";
+import { dirname } from "node:path";
+import { cairnDir, appendMissionJournal, findActiveMission, readMissionState, readRoadmap, writeMissionState, } from "@isaacriehm/cairn-state";
 import { requireBootstrap } from "../bootstrap-guard.js";
 import { mcpError } from "../errors.js";
 import { missionAdvanceInput } from "../schemas.js";
@@ -12,7 +12,7 @@ import { advanceMissionPhase as advancePhase } from "../../missions/index.js";
  * / `aborted`). Returns "unknown" when the file is missing or unreadable.
  */
 function readGraduatedOutcome(repoRoot, taskId) {
-    const statusPath = join(repoRoot, ".cairn", "tasks", "done", taskId, "status.yaml");
+    const statusPath = cairnDir(repoRoot, "tasks", "done", taskId, "status.yaml");
     if (!existsSync(statusPath))
         return "unknown";
     try {
@@ -37,7 +37,7 @@ function writeMissionPhaseDefer(repoRoot, missionId, phaseId, hours) {
         deferred_at: now.toISOString(),
         deferred_until: until.toISOString(),
     };
-    const path = join(repoRoot, ".cairn", ".mission-phase-deferred-until");
+    const path = cairnDir(repoRoot, ".mission-phase-deferred-until");
     mkdirSync(dirname(path), { recursive: true });
     writeFileSync(path, JSON.stringify(payload, null, 2), "utf8");
     return until.toISOString();
@@ -53,7 +53,7 @@ function writeMissionPhaseDefer(repoRoot, missionId, phaseId, hours) {
  * the 24h expiry rolled past.
  */
 export function clearMissionPhaseDeferIfMatches(repoRoot, match) {
-    const path = join(repoRoot, ".cairn", ".mission-phase-deferred-until");
+    const path = cairnDir(repoRoot, ".mission-phase-deferred-until");
     if (!existsSync(path))
         return false;
     try {

package/dist/mcp/tools/mission-advance.js.map

@@ -1 +1 @@
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