grounder 0.3.0 → 0.5.0

package/dist/agents/hook-runtime.d.ts

@@ -16,7 +16,7 @@
  * [npm/cli#9244](https://github.com/npm/cli/issues/9244).
  *
  * ## Design
- * On `vault init`, materialize this package's `dist/` at
+ * On `setup`, materialize this package's `dist/` at
  * `~/.grounder/runtime/dist/` and point both host hook configs *and* the
  * commands copied into `~/.cursor/commands/` / `~/.claude/commands/` at:
  *   `process.execPath` + `~/.grounder/runtime/dist/cli.js` + `<subcommand> …`
@@ -29,11 +29,11 @@
  * - **Durable source** (monorepo checkout, global install, linked devDependency) →
  *   **symlink** `dist/` straight to the source. `pnpm build` / upgrading the
  *   global install overwrites that same path in place, so hooks and commands
- *   pick up new code immediately — no re-run of `vault init` ever needed.
+ *   pick up new code immediately — no re-run of `setup` ever needed.
  * - **Ephemeral source** (bare `npx grounder …`, no install — each invocation
  *   resolves to an immutable, version-keyed npx cache dir that can be evicted
  *   or swapped out from under a symlink) → **copy** `dist/`. Re-run
- *   `grounder vault init <vault>` after upgrading to refresh; this is an
+ *   `grounder setup <vault>` after upgrading to refresh; this is an
  *   inherent limitation of using npx with no install for something that must
  *   persist, not something we can engineer around.
  *

package/dist/agents/hook-runtime.js

@@ -16,7 +16,7 @@
  * [npm/cli#9244](https://github.com/npm/cli/issues/9244).
  *
  * ## Design
- * On `vault init`, materialize this package's `dist/` at
+ * On `setup`, materialize this package's `dist/` at
  * `~/.grounder/runtime/dist/` and point both host hook configs *and* the
  * commands copied into `~/.cursor/commands/` / `~/.claude/commands/` at:
  *   `process.execPath` + `~/.grounder/runtime/dist/cli.js` + `<subcommand> …`
@@ -29,11 +29,11 @@
  * - **Durable source** (monorepo checkout, global install, linked devDependency) →
  *   **symlink** `dist/` straight to the source. `pnpm build` / upgrading the
  *   global install overwrites that same path in place, so hooks and commands
- *   pick up new code immediately — no re-run of `vault init` ever needed.
+ *   pick up new code immediately — no re-run of `setup` ever needed.
  * - **Ephemeral source** (bare `npx grounder …`, no install — each invocation
  *   resolves to an immutable, version-keyed npx cache dir that can be evicted
  *   or swapped out from under a symlink) → **copy** `dist/`. Re-run
- *   `grounder vault init <vault>` after upgrading to refresh; this is an
+ *   `grounder setup <vault>` after upgrading to refresh; this is an
  *   inherent limitation of using npx with no install for something that must
  *   persist, not something we can engineer around.
  *
@@ -343,7 +343,7 @@ export async function installHookRuntime(options) {
     const cliPath = runtimeCliPath(options.homeDir);
     const existed = await fileExists(cliPath);
     if (!(await fileExists(path.join(sourceDistDir, "cli.js")))) {
-        throw new Error(`Grounder dist missing at ${sourceDistDir}. Run \`pnpm build\` (or install a published package) before vault init.`);
+        throw new Error(`Grounder dist missing at ${sourceDistDir}. Run \`pnpm build\` (or install a published package) before setup.`);
     }
     await mkdir(runtimeDir, { recursive: true });
     // Stage into a sibling path first, then swap. If symlink/cp fails, the live

package/dist/agents/hook-runtime.js.map

@@ -1 +1 @@
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package/dist/agents/install-command.d.ts

@@ -1,7 +1,6 @@
 import type { AgentInstallOptions, ArtifactStatus } from "./types.js";
 export interface InstallCommandFileOptions extends AgentInstallOptions {
     agentId: string;
-    commandsSchema: number;
     templateDir: string;
     commandsDir: string;
     filename: string;
@@ -28,7 +27,6 @@ export declare function recordCommandFileHashes(opts: {
     agentId: string;
     commandsSchema: number;
     files: Record<string, {
-        schema: number;
         hash: string;
     }>;
     homeDir?: string;

package/dist/agents/install-command.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"install-command.d.ts","sourceRoot":"","sources":["../../src/agents/install-command.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,mBAAmB,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAEtE,MAAM,WAAW,yBAA0B,SAAQ,mBAAmB;IACpE,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,wBAAwB;IACvC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,cAAc,CAAC;IACvB,2EAA2E;IAC3E,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED;;;;;;GAMG;AACH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,yBAAyB,GAC9B,OAAO,CAAC,wBAAwB,CAAC,CAuCnC;AAED;;;GAGG;AACH,wBAAsB,uBAAuB,CAAC,IAAI,EAAE;IAClD,OAAO,EAAE,MAAM,CAAC;IAChB,cAAc,EAAE,MAAM,CAAC;IACvB,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACxC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB,GAAG,OAAO,CAAC,IAAI,CAAC,CAWhB"}

package/dist/agents/install-command.js.map

@@ -1 +1 @@
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package/dist/cli.js

@@ -6,17 +6,19 @@ import { runDoctor } from "./commands/doctor.js";
 import { runHandoffList } from "./commands/handoff/list.js";
 import { runHandoffPeek } from "./commands/handoff/peek.js";
 import { runHandoff } from "./commands/handoff.js";
+import { runLink } from "./commands/link.js";
 import { runMigrate } from "./commands/migrate.js";
+import { runNoteList } from "./commands/note/list.js";
 import { runNote } from "./commands/note.js";
 import { runPathLogs } from "./commands/path/logs.js";
 import { runPathNotes } from "./commands/path/notes.js";
 import { runPathPlans } from "./commands/path/plans.js";
 import { runPlanList } from "./commands/plan/list.js";
 import { runPlan } from "./commands/plan.js";
-import { runRepoInit } from "./commands/repo/init.js";
+import { runSearch } from "./commands/search.js";
+import { runSetup } from "./commands/setup.js";
 import { runStatus } from "./commands/status.js";
 import { notifyUpgradeIfNeeded } from "./commands/upgrade-banner.js";
-import { runVaultInit } from "./commands/vault/init.js";
 import { printCommandHelpById, printFullHelp, printSynopsis, runHelp, wantsHelp } from "./help.js";
 const pkgRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "..");
 const pkg = JSON.parse(readFileSync(path.join(pkgRoot, "package.json"), "utf8"));
@@ -55,18 +57,18 @@ async function main() {
     const skipUpgradeBanner = wantsHelp(args) ||
         (command === "handoff" && rest[0] === "peek") ||
         command === "migrate" ||
-        (command === "vault" && rest[0] === "init");
+        command === "setup";
     if (!skipUpgradeBanner) {
         await notifyUpgradeIfNeeded();
     }
-    if (command === "vault") {
-        if (rest[0] === "init") {
-            process.exit(await runVaultInit(rest.slice(1)));
-        }
-        exitParentTopic("vault", wantsHelp(rest) || rest.length === 0);
+    if (command === "setup") {
+        process.exit(await runSetup(rest));
+    }
+    if (command === "link") {
+        process.exit(await runLink(rest));
     }
-    if (command === "init") {
-        process.exit(await runRepoInit(rest));
+    if (command === "note" && rest[0] === "list") {
+        process.exit(await runNoteList(rest.slice(1)));
     }
     if (command === "note") {
         process.exit(await runNote(rest));
@@ -86,6 +88,9 @@ async function main() {
     if (command === "plan") {
         process.exit(await runPlan(rest));
     }
+    if (command === "search") {
+        process.exit(await runSearch(rest));
+    }
     if (command === "path") {
         if (rest[0] === "notes") {
             process.exit(await runPathNotes(rest.slice(1)));

package/dist/cli.js.map

@@ -1 +1 @@
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package/dist/commands/apply-agent-installs.d.ts

@@ -2,7 +2,7 @@ import type { AgentAdapter, AgentInstallResult, ArtifactStatus } from "../agents
 export interface ApplyAgentInstallsOptions {
     agents: AgentAdapter[];
     force?: boolean;
-    /** Explicitly install/refresh session hooks (vault init --hooks / migrate --hooks). */
+    /** Explicitly install/refresh session hooks (setup --hooks / migrate --hooks). */
     hooks?: boolean;
     /**
      * When true (migrate), also refresh hooks that were previously recorded or
@@ -28,7 +28,7 @@ export interface ApplyAgentInstallsResult {
 }
 /**
  * Materialize runtime + install/refresh agent command (and optional hook)
- * artifacts. Shared by `grounder vault init` and `grounder migrate`.
+ * artifacts. Shared by `grounder setup` and `grounder migrate`.
  */
 export declare function applyAgentInstalls(opts: ApplyAgentInstallsOptions): Promise<ApplyAgentInstallsResult>;
 //# sourceMappingURL=apply-agent-installs.d.ts.map

package/dist/commands/apply-agent-installs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"apply-agent-installs.d.ts","sourceRoot":"","sources":["../../src/commands/apply-agent-installs.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,YAAY,EAAE,kBAAkB,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAS3F,MAAM,WAAW,yBAAyB;IACxC,MAAM,EAAE,YAAY,EAAE,CAAC;IACvB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,uFAAuF;IACvF,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB;;;;OAIG;IACH,qBAAqB,CAAC,EAAE,OAAO,CAAC;IAChC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,YAAY,CAAC;IACpB,QAAQ,EAAE,kBAAkB,CAAC;IAC7B,KAAK,CAAC,EAAE,kBAAkB,CAAC;CAC5B;AAED,MAAM,WAAW,wBAAwB;IACvC,OAAO,CAAC,EAAE;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,cAAc,CAAC;QAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAAA;KAAE,CAAC;IAChF,MAAM,EAAE,gBAAgB,EAAE,CAAC;CAC5B;AA+DD;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,yBAAyB,GAC9B,OAAO,CAAC,wBAAwB,CAAC,CA6FnC"}
+{"version":3,"file":"apply-agent-installs.d.ts","sourceRoot":"","sources":["../../src/commands/apply-agent-installs.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,YAAY,EAAE,kBAAkB,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAS3F,MAAM,WAAW,yBAAyB;IACxC,MAAM,EAAE,YAAY,EAAE,CAAC;IACvB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,kFAAkF;IAClF,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB;;;;OAIG;IACH,qBAAqB,CAAC,EAAE,OAAO,CAAC;IAChC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,YAAY,CAAC;IACpB,QAAQ,EAAE,kBAAkB,CAAC;IAC7B,KAAK,CAAC,EAAE,kBAAkB,CAAC;CAC5B;AAED,MAAM,WAAW,wBAAwB;IACvC,OAAO,CAAC,EAAE;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,cAAc,CAAC;QAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAAA;KAAE,CAAC;IAChF,MAAM,EAAE,gBAAgB,EAAE,CAAC;CAC5B;AA+DD;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,yBAAyB,GAC9B,OAAO,CAAC,wBAAwB,CAAC,CA6FnC"}

package/dist/commands/apply-agent-installs.js

@@ -56,7 +56,7 @@ function hookLabel(status, artifactPath, dryRun) {
 }
 /**
  * Materialize runtime + install/refresh agent command (and optional hook)
- * artifacts. Shared by `grounder vault init` and `grounder migrate`.
+ * artifacts. Shared by `grounder setup` and `grounder migrate`.
  */
 export async function applyAgentInstalls(opts) {
     const force = opts.force ?? false;

package/dist/commands/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAqCA,MAAM,WAAW,aAAa;IAC5B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,sDAAsD;IACtD,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AA2hBD,wBAAsB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAQ/D;AAED,wBAAsB,oBAAoB,CAAC,OAAO,GAAE,aAAkB,GAAG,OAAO,CAAC,MAAM,CAAC,CAiBvF"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAqCA,MAAM,WAAW,aAAa;IAC5B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,sDAAsD;IACtD,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAipBD,wBAAsB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAQ/D;AAED,wBAAsB,oBAAoB,CAAC,OAAO,GAAE,aAAkB,GAAG,OAAO,CAAC,MAAM,CAAC,CAyBvF"}

package/dist/commands/doctor.js

@@ -5,7 +5,7 @@ import { resolveAgents } from "../agents/index.js";
 import { findGitRoot } from "../connector/git.js";
 import { homeConfigPath, readHomeConfig, withHomeDir } from "../connector/home.js";
 import { findLinkedRepoRoot, readRepoConfig } from "../connector/repo.js";
-import { isHooksSchemaAhead, isHooksSchemaBehind, readGrounderState, recordedCommandsSchema, recordedHooksSchema, statePath, } from "../connector/state.js";
+import { isHooksSchemaAhead, readGrounderState, recordedCommandsSchema, recordedHooksSchema, statePath, } from "../connector/state.js";
 import { isUnsupportedSchemaError } from "../connector/unsupported-schema.js";
 import { resolveLogsDir, resolveNotesDir, resolvePlansDir, resolveVaultRoot, } from "../connector/vault.js";
 import { helpExitCode } from "../help.js";
@@ -14,12 +14,13 @@ import { fileExists, isExecutable } from "../util/fs.js";
 import { flagBool, parseArgs } from "../util/parse-args.js";
 import { projectsParent } from "../vault/layout.js";
 import { failCheck, okCheck, warnCheck } from "./check.js";
+import { fixArrow, writeSection } from "./output.js";
 import { packageVersionNotice } from "./package-version-notice.js";
-const VAULT_INIT = "grounder vault init <path>";
+const VAULT_INIT = "grounder setup <path>";
 const MIGRATE = "grounder migrate";
 const MIGRATE_FORCE = "grounder migrate --force";
 const MIGRATE_HOOKS = "grounder migrate --hooks";
-const REPO_INIT = "grounder init";
+const REPO_INIT = "grounder link";
 const UPGRADE_GROUNDER = "upgrade grounder";
 /** First baked Node path that is missing or not executable; `null` if all ok / none found. */
 async function firstDanglingRuntimeNode(nodePaths) {
@@ -30,13 +31,6 @@ async function firstDanglingRuntimeNode(nodePaths) {
     }
     return null;
 }
-/**
- * Commands installed before Grounder 0.3 have no per-file content hash, so
- * migrate cannot tell stock files from user edits — `--force` is required once.
- */
-function commandsMigrateHint(recordedSchema) {
-    return recordedSchema === 0 ? MIGRATE_FORCE : MIGRATE;
-}
 async function isDirectory(dirPath) {
     try {
         const info = await stat(dirPath);
@@ -49,11 +43,10 @@ async function isDirectory(dirPath) {
 function formatCheck(check) {
     const level = check.level.padEnd(4);
     const id = check.id.padEnd(18);
-    const fix = check.fix ? ` → ${check.fix}` : "";
-    return `  ${level}  ${id}  ${check.message}${fix}\n`;
+    return `  ${level}  ${id}  ${check.message}${fixArrow(check.fix)}\n`;
 }
-function writeSection(title, checks) {
-    process.stdout.write(`${title}\n`);
+function writeChecks(title, checks) {
+    writeSection(title);
     for (const check of checks) {
         process.stdout.write(formatCheck(check));
     }
@@ -103,7 +96,7 @@ async function checkVault(home) {
     const vaultRoot = resolveVaultRoot(home);
     if (!(await isDirectory(vaultRoot))) {
         return {
-            check: failCheck("vault", `${vaultRoot} missing or not a directory`, "Fix path or re-run vault init"),
+            check: failCheck("vault", `${vaultRoot} missing or not a directory`, "Fix path or re-run setup"),
             vaultRoot: null,
         };
     }
@@ -160,33 +153,17 @@ function checkPackageVersion(state) {
     }
     return warnCheck("package-version", notice.message, notice.fix);
 }
-function commandsSchemaStale(agent, state, 
-/** When false, state was unreadable — don't invent a schema-0 warn. */
-stateReadable) {
-    if (!stateReadable) {
-        return false;
-    }
-    return recordedCommandsSchema(state, agent.id) < agent.commandsSchema;
-}
 function commandsSchemaAhead(agent, state, stateReadable) {
     if (!stateReadable) {
         return false;
     }
     return recordedCommandsSchema(state, agent.id) > agent.commandsSchema;
 }
-/**
- * Whether installed session hooks are behind this Grounder.
- * Only call when those hook files are already present.
- *
- * No hooks version in state counts as version 0, so older hook installs still
- * suggest migrate. Peek/status use {@link isInstallSchemaStale} instead, which
- * does not treat "hooks never enabled" as behind.
- */
-function hooksSchemaStale(agent, state, stateReadable) {
-    if (!stateReadable || agent.hooksSchema === undefined) {
+function commandsSchemaBehind(agent, state, stateReadable) {
+    if (!stateReadable || !state?.agents[agent.id]) {
         return false;
     }
-    return isHooksSchemaBehind(state?.agents[agent.id]?.hooksSchema, agent.hooksSchema);
+    return recordedCommandsSchema(state, agent.id) < agent.commandsSchema;
 }
 function hooksSchemaAhead(agent, state, stateReadable) {
     if (!stateReadable || agent.hooksSchema === undefined) {
@@ -194,6 +171,56 @@ function hooksSchemaAhead(agent, state, stateReadable) {
     }
     return isHooksSchemaAhead(state?.agents[agent.id]?.hooksSchema, agent.hooksSchema);
 }
+/** Match {@link isInstallSchemaStale}: only when a hooks version was recorded. */
+function hooksSchemaBehindInLedger(agent, state, stateReadable) {
+    if (!stateReadable || agent.hooksSchema === undefined) {
+        return false;
+    }
+    const recorded = state?.agents[agent.id]?.hooksSchema;
+    if (recorded === undefined) {
+        return false;
+    }
+    return recorded < agent.hooksSchema;
+}
+/**
+ * When on-disk files already match templates but `state.json` schema numbers
+ * lag, surface the same migrate hint `status` shows for ledger staleness.
+ */
+function applyLedgerSchemaLag(check, opts) {
+    if (check.level !== "ok" || !opts.behind) {
+        return check;
+    }
+    return warnCheck(opts.id, `${opts.agentName}: ${opts.kind} schema behind in ledger (recorded ${opts.recorded}, current ${opts.current}; files match)`, MIGRATE);
+}
+/**
+ * Map migrate dry-run artifact statuses onto a doctor check.
+ * `modified` needs `--force`; `overwritten` / `created` would write on plain migrate.
+ * Only `skipped` counts as up to date.
+ */
+function checkFromInstallPreview(id, agentName, kind, preview, upToDateMessage) {
+    const statuses = Object.values(preview.artifacts);
+    const modified = statuses.filter((s) => s === "modified").length;
+    const created = statuses.filter((s) => s === "created").length;
+    const overwritten = statuses.filter((s) => s === "overwritten").length;
+    const wouldWrite = created + overwritten;
+    if (modified === 0 && wouldWrite === 0) {
+        return okCheck(id, upToDateMessage);
+    }
+    if (modified === 0) {
+        return warnCheck(id, `${agentName}: ${pendingWriteMessage(kind, created, overwritten)}`, MIGRATE);
+    }
+    return warnCheck(id, `${agentName}: ${modified} ${kind} locally modified (needs --force to refresh)` +
+        (wouldWrite > 0 ? `, ${wouldWrite} would auto-update` : ""), MIGRATE_FORCE);
+}
+function pendingWriteMessage(kind, created, overwritten) {
+    if (created > 0 && overwritten > 0) {
+        return `${created + overwritten} ${kind} would install or update on next migrate`;
+    }
+    if (created > 0) {
+        return `${created} ${kind} would install on next migrate`;
+    }
+    return `${overwritten} ${kind} would update on next migrate`;
+}
 async function checkAgentArtifacts(state, stateReadable, homeDir) {
     const agents = await resolveAgents();
     const checks = [];
@@ -221,9 +248,23 @@ async function checkAgentArtifacts(state, stateReadable, homeDir) {
                 const recorded = recordedCommandsSchema(state, agent.id);
                 checks.push(failCheck(id, `${agent.name} commands schema newer than this grounder (recorded ${recorded}, supported ${agent.commandsSchema})`, UPGRADE_GROUNDER));
             }
-            else if (commandsSchemaStale(agent, state, stateReadable)) {
-                const recorded = recordedCommandsSchema(state, agent.id);
-                checks.push(warnCheck(id, `${agent.name} commands schema stale (recorded ${recorded}, current ${agent.commandsSchema}) — migrate`, commandsMigrateHint(recorded)));
+            else if (stateReadable) {
+                try {
+                    const preview = await agent.install({ force: false, dryRun: true, homeDir });
+                    const previewCheck = checkFromInstallPreview(id, agent.name, "command file(s)", preview, `${agent.name} command files up to date`);
+                    checks.push(applyLedgerSchemaLag(previewCheck, {
+                        id,
+                        agentName: agent.name,
+                        kind: "commands",
+                        recorded: recordedCommandsSchema(state, agent.id),
+                        current: agent.commandsSchema,
+                        behind: commandsSchemaBehind(agent, state, stateReadable),
+                    }));
+                }
+                catch (error) {
+                    const detail = error instanceof Error ? error.message : String(error);
+                    checks.push(warnCheck(id, `${agent.name}: could not verify command drift (${detail})`, MIGRATE));
+                }
             }
             else {
                 checks.push(okCheck(id, `${agent.name} command files present`));
@@ -256,6 +297,9 @@ async function checkAgentHooks(state, stateReadable, homeDir) {
     let anyHooksInstalled = false;
     const commandsPresent = await Promise.all(agents.map((agent) => Promise.all(agent.expectedArtifacts(homeDir).map((p) => fileExists(p)))));
     const anyCommandsInstalled = commandsPresent.some((present) => present.some(Boolean));
+    // Shared runtime staleness alone makes installHooks dry-run report would-update;
+    // keep that as a single hook-runtime warn below instead of doubling up.
+    const runtimeStale = await isHookRuntimeStale(homeDir);
     for (const agent of agents) {
         if (!agent.expectedHookArtifacts) {
             continue;
@@ -280,9 +324,26 @@ async function checkAgentHooks(state, stateReadable, homeDir) {
                 const recorded = recordedHooksSchema(state, agent.id);
                 checks.push(failCheck(id, `${agent.name} hooks schema newer than this grounder (recorded ${recorded}, supported ${agent.hooksSchema})`, UPGRADE_GROUNDER));
             }
-            else if (hooksSchemaStale(agent, state, stateReadable)) {
-                const recorded = recordedHooksSchema(state, agent.id);
-                checks.push(warnCheck(id, `${agent.name} hooks schema stale (recorded ${recorded}, current ${agent.hooksSchema}) — migrate`, MIGRATE));
+            else if (runtimeStale) {
+                checks.push(okCheck(id, `${agent.name} session hook installed`));
+            }
+            else if (stateReadable && agent.installHooks) {
+                try {
+                    const preview = await agent.installHooks({ force: false, dryRun: true, homeDir });
+                    const previewCheck = checkFromInstallPreview(id, agent.name, "session hook file(s)", preview, `${agent.name} session hook up to date`);
+                    checks.push(applyLedgerSchemaLag(previewCheck, {
+                        id,
+                        agentName: agent.name,
+                        kind: "hooks",
+                        recorded: recordedHooksSchema(state, agent.id),
+                        current: agent.hooksSchema ?? 0,
+                        behind: hooksSchemaBehindInLedger(agent, state, stateReadable),
+                    }));
+                }
+                catch (error) {
+                    const detail = error instanceof Error ? error.message : String(error);
+                    checks.push(warnCheck(id, `${agent.name}: could not verify session hook drift (${detail})`, MIGRATE));
+                }
             }
             else {
                 checks.push(okCheck(id, `${agent.name} session hook installed`));
@@ -293,7 +354,7 @@ async function checkAgentHooks(state, stateReadable, homeDir) {
         }
     }
     if (anyHooksInstalled || anyCommandsInstalled) {
-        if (await isHookRuntimeStale(homeDir)) {
+        if (runtimeStale) {
             checks.push(warnCheck("hook-runtime", "hook runtime stale or missing (re-run after upgrading, especially bare npx)", MIGRATE));
         }
         else {
@@ -310,8 +371,6 @@ async function runMachineChecks(homeDir) {
     // Corrupt ledger: don't invent schema-0 migrate warns on top of the fail.
     const stateReadable = stateCheck.level !== "fail";
     const packageVersionCheck = checkPackageVersion(state);
-    const agentChecks = await checkAgentArtifacts(state, stateReadable, homeDir);
-    const hookChecks = await checkAgentHooks(state, stateReadable, homeDir);
     return {
         checks: [
             homeCheck,
@@ -319,12 +378,17 @@ async function runMachineChecks(homeDir) {
             projectsCheck,
             stateCheck,
             ...(packageVersionCheck ? [packageVersionCheck] : []),
-            ...agentChecks,
-            ...hookChecks,
         ],
+        state,
+        stateReadable,
         home,
     };
 }
+async function runAgentChecks(state, stateReadable, homeDir) {
+    const agentChecks = await checkAgentArtifacts(state, stateReadable, homeDir);
+    const hookChecks = await checkAgentHooks(state, stateReadable, homeDir);
+    return [...agentChecks, ...hookChecks];
+}
 async function runProjectChecks(cwd, home) {
     const checks = [];
     const gitRoot = await findGitRoot(cwd);
@@ -337,7 +401,10 @@ async function runProjectChecks(cwd, home) {
         checks.push(failCheck("plans-dir", "cannot resolve plans/ (no repo config)", REPO_INIT));
     }
     else {
-        checks.push(okCheck("repo-config", `repo config present (${path.join(linkedRoot, ".grounder.json")})`));
+        const ancestorNote = linkedRoot === cwd
+            ? ""
+            : ` — ancestor of ${cwd}; this folder itself is unlinked (grounder link here would create a separate project)`;
+        checks.push(okCheck("repo-config", `repo config present (${path.join(linkedRoot, ".grounder.json")})${ancestorNote}`));
         let repo = null;
         let repoUnsupported = false;
         try {
@@ -405,13 +472,16 @@ export async function runDoctor(argv) {
 export async function runDoctorWithOptions(options = {}) {
     return withHomeDir(options.homeDir, async () => {
         const cwd = path.resolve(options.cwd ?? process.cwd());
-        const { checks: machineChecks, home } = await runMachineChecks(options.homeDir);
+        const { checks: machineChecks, state, stateReadable, home, } = await runMachineChecks(options.homeDir);
+        const agentChecks = await runAgentChecks(state, stateReadable, options.homeDir);
         const projectChecks = options.global ? [] : await runProjectChecks(cwd, home);
-        const checks = [...machineChecks, ...projectChecks];
-        writeSection("Machine", machineChecks);
+        const checks = [...machineChecks, ...agentChecks, ...projectChecks];
+        writeChecks("Machine", machineChecks);
+        process.stdout.write("\n");
+        writeChecks("Agents", agentChecks);
         if (!options.global) {
             process.stdout.write("\n");
-            writeSection("Project", projectChecks);
+            writeChecks("Project", projectChecks);
         }
         process.stdout.write("\n");
         process.stdout.write(summarize(checks));