@lannguyensi/harness 0.38.0 → 0.39.0

package/dist/cli/apply/generate-settings.js

@@ -43,7 +43,12 @@
 //   - Within an event, groups sorted by (matcher, command).
 //   - Within a group, the inner hooks[] preserves matcher-grouping order
 //     and is sorted by command for the same reason.
+import { expandHome } from "../../runtime/expand-home.js";
 export const DEFAULT_BUDGET_MS = 30_000;
+/** The manifest `tools.mcp[]` entry name that grounding enforcement keys off. */
+export const GROUNDING_MCP_SERVER_NAME = "grounding-mcp";
+/** The env var grounding-mcp's ledger-bridge reads for the evidence-ledger DB path. */
+export const EVIDENCE_LEDGER_DB_ENV = "EVIDENCE_LEDGER_DB";
 export function generateSettings(manifest) {
     return generateSettingsWithWarnings(manifest).root;
 }
@@ -74,6 +79,7 @@ export function generateSettingsWithWarnings(manifest, extras = {}) {
         out.hooks[event] = buildGroups(hooks);
     }
     const mcp = buildMcpServers(manifest.tools.mcp, warnings);
+    projectGroundingEnv(manifest, mcp, extras.homeDir);
     if (Object.keys(mcp).length > 0)
         out.mcpServers = mcp;
     const permissions = compactPermissions(extras.packPermissions);
@@ -147,6 +153,53 @@ export function buildMcpServers(entries, warnings) {
     }
     return out;
 }
+/**
+ * Wire the manifest's `grounding:` section into the grounding-mcp server
+ * entry (task 129e1b94, harness-review-2026-07-01/grounding-decorative).
+ *
+ * `grounding.evidence_ledger.path` becomes the `EVIDENCE_LEDGER_DB` env on
+ * the `tools.mcp[grounding-mcp]` entry — the exact variable grounding-mcp's
+ * ledger-bridge reads (agent-grounding
+ * packages/grounding-mcp/src/ledger-bridge.ts). This makes `grounding:` the
+ * section that CONFIGURES the grounding-mcp entry instead of a decorative
+ * namesake, resolving the naming collision the 2026-07-01 review flagged.
+ *
+ * Rules:
+ * - Projection only fires when a grounding-mcp entry exists; without one
+ *   there is no consumer (doctor surfaces that inertness separately).
+ * - An operator-declared `env.EVIDENCE_LEDGER_DB` on the entry wins — an
+ *   explicit override is never clobbered (doctor warns when it diverges
+ *   from `grounding.evidence_ledger.path`).
+ * - The projected value is `~`-expanded to an absolute path, so the
+ *   literal-tilde child-process footgun (agent-tasks/42d224a6, the very
+ *   warning above in buildMcpServers) cannot re-enter via this path.
+ * - `retention_days`, `policies_source`, and `session.*` stay RESERVED:
+ *   nothing consumes them yet (evidence-ledger has no retention pruning),
+ *   and projecting an env no server reads would be decorative again. See
+ *   the status comments in src/schema/grounding.ts.
+ */
+export function projectGroundingEnv(manifest, mcp, homeDir) {
+    const server = mcp[GROUNDING_MCP_SERVER_NAME];
+    if (!server)
+        return;
+    const env = server.env ?? {};
+    // Truthiness (not `=== undefined`) on purpose: an empty-string operator
+    // "override" would project an empty ledger path, which guarantees a
+    // broken ledger — treat it as absent and let the manifest value apply.
+    if (!env[EVIDENCE_LEDGER_DB_ENV]) {
+        env[EVIDENCE_LEDGER_DB_ENV] = groundingLedgerEnvValue(manifest, homeDir);
+        server.env = env;
+    }
+}
+/**
+ * The value apply projects for `EVIDENCE_LEDGER_DB`: the manifest's
+ * `grounding.evidence_ledger.path`, `~`-expanded to an absolute path.
+ * Shared with adopt's manifest→settings projection so the apply→adopt
+ * round-trip stays drift-free by construction.
+ */
+export function groundingLedgerEnvValue(manifest, homeDir) {
+    return expandHome(manifest.grounding.evidence_ledger.path, homeDir);
+}
 // Translate manifest `memory.router` into a synthetic UserPromptSubmit
 // hook so per-prompt context augmentation actually fires alongside the
 // understanding-gate hook. Returns null when memory.router is absent or

package/dist/cli/apply/generate-settings.js.map

@@ -1 +1 @@
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package/dist/cli/diff/git.d.ts

@@ -4,3 +4,16 @@ export interface GitContext {
 }
 export declare function locateGitContext(manifestPath: string): GitContext;
 export declare function readManifestAtRef(ctx: GitContext, ref: string): string;
+/**
+ * Repo-relative path for `absPath` in git's forward-slash form, or null
+ * when the file lives outside the repo work tree (e.g. an override layer
+ * under a ~/.harness home that is not the manifest's repo).
+ */
+export declare function repoRelativePath(ctx: GitContext, absPath: string): string | null;
+/**
+ * Read a repo file at a git ref, or null when it does not exist at that
+ * ref. Callers must have validated the ref itself first (the base-manifest
+ * read via {@link readManifestAtRef} hard-errors on a bad ref), so a null
+ * here means "file absent at ref", not "bad ref".
+ */
+export declare function readFileAtRefOrNull(ctx: GitContext, ref: string, relPath: string): string | null;

package/dist/cli/diff/git.js

@@ -29,4 +29,29 @@ export function readManifestAtRef(ctx, ref) {
         throw new HarnessExitError(`cannot read ${ctx.manifestRelPath} at git ref "${ref}": ${message}`, EX_USAGE);
     }
 }
+/**
+ * Repo-relative path for `absPath` in git's forward-slash form, or null
+ * when the file lives outside the repo work tree (e.g. an override layer
+ * under a ~/.harness home that is not the manifest's repo).
+ */
+export function repoRelativePath(ctx, absPath) {
+    const rel = path.relative(ctx.root, path.resolve(absPath));
+    if (rel.startsWith("..") || path.isAbsolute(rel))
+        return null;
+    return rel.split(path.sep).join("/");
+}
+/**
+ * Read a repo file at a git ref, or null when it does not exist at that
+ * ref. Callers must have validated the ref itself first (the base-manifest
+ * read via {@link readManifestAtRef} hard-errors on a bad ref), so a null
+ * here means "file absent at ref", not "bad ref".
+ */
+export function readFileAtRefOrNull(ctx, ref, relPath) {
+    try {
+        return runGit(["show", `${ref}:${relPath}`], ctx.root);
+    }
+    catch {
+        return null;
+    }
+}
 //# sourceMappingURL=git.js.map

package/dist/cli/diff/git.js.map

@@ -1 +1 @@
-{"version":3,"file":"git.js","sourceRoot":"","sources":["../../../src/cli/diff/git.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,cAAc,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAO9E,SAAS,MAAM,CAAC,IAAc,EAAE,GAAW;IACzC,OAAO,YAAY,CAAC,KAAK,EAAE,IAAI,EAAE;QAC/B,GAAG;QACH,QAAQ,EAAE,MAAM;QAChB,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC;KAClC,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,YAAoB;IACnD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC;IACrD,IAAI,IAAY,CAAC;IACjB,IAAI,CAAC;QACH,IAAI,GAAG,MAAM,CAAC,CAAC,WAAW,EAAE,iBAAiB,CAAC,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;IAC9D,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,IAAI,gBAAgB,CACxB,2BAA2B,GAAG,mCAAoC,GAAa,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,EAChG,cAAc,CACf,CAAC;IACJ,CAAC;IACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC;IAChE,OAAO,EAAE,IAAI,EAAE,eAAe,EAAE,OAAO,EAAE,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,GAAe,EAAE,GAAW;IAC5D,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,CAAC,MAAM,EAAE,GAAG,GAAG,IAAI,GAAG,CAAC,eAAe,EAAE,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC;IACrE,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,OAAO,GAAI,GAAmC,CAAC,MAAM,EAAE,IAAI,EAAE,IAAK,GAAa,CAAC,OAAO,CAAC;QAC9F,MAAM,IAAI,gBAAgB,CACxB,eAAe,GAAG,CAAC,eAAe,gBAAgB,GAAG,MAAM,OAAO,EAAE,EACpE,QAAQ,CACT,CAAC;IACJ,CAAC;AACH,CAAC"}
+{"version":3,"file":"git.js","sourceRoot":"","sources":["../../../src/cli/diff/git.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,cAAc,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAO9E,SAAS,MAAM,CAAC,IAAc,EAAE,GAAW;IACzC,OAAO,YAAY,CAAC,KAAK,EAAE,IAAI,EAAE;QAC/B,GAAG;QACH,QAAQ,EAAE,MAAM;QAChB,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC;KAClC,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,YAAoB;IACnD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC;IACrD,IAAI,IAAY,CAAC;IACjB,IAAI,CAAC;QACH,IAAI,GAAG,MAAM,CAAC,CAAC,WAAW,EAAE,iBAAiB,CAAC,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;IAC9D,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,IAAI,gBAAgB,CACxB,2BAA2B,GAAG,mCAAoC,GAAa,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,EAChG,cAAc,CACf,CAAC;IACJ,CAAC;IACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC;IAChE,OAAO,EAAE,IAAI,EAAE,eAAe,EAAE,OAAO,EAAE,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,GAAe,EAAE,GAAW;IAC5D,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,CAAC,MAAM,EAAE,GAAG,GAAG,IAAI,GAAG,CAAC,eAAe,EAAE,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC;IACrE,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,OAAO,GAAI,GAAmC,CAAC,MAAM,EAAE,IAAI,EAAE,IAAK,GAAa,CAAC,OAAO,CAAC;QAC9F,MAAM,IAAI,gBAAgB,CACxB,eAAe,GAAG,CAAC,eAAe,gBAAgB,GAAG,MAAM,OAAO,EAAE,EACpE,QAAQ,CACT,CAAC;IACJ,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,gBAAgB,CAAC,GAAe,EAAE,OAAe;IAC/D,MAAM,GAAG,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC;IAC3D,IAAI,GAAG,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC;QAAE,OAAO,IAAI,CAAC;IAC9D,OAAO,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,mBAAmB,CACjC,GAAe,EACf,GAAW,EACX,OAAe;IAEf,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,CAAC,MAAM,EAAE,GAAG,GAAG,IAAI,OAAO,EAAE,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC;IACzD,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC"}

package/dist/cli/diff/index.d.ts

@@ -9,6 +9,13 @@ export interface DiffResult {
     output: string;
     before: Manifest;
     after: Manifest;
+    /**
+     * Override-layer diagnostics (task b2660f9e): one entry per active
+     * layer that is not versioned in the manifest's repo and was therefore
+     * treated as constant on both sides of the comparison. Callers print
+     * these to stderr so the diff on stdout stays clean.
+     */
+    warnings: string[];
 }
 export declare function diff(opts: DiffOptions): DiffResult;
 export { diffManifests, formatDiff } from "./engine.js";

package/dist/cli/diff/index.js

@@ -1,17 +1,20 @@
+import * as fs from "node:fs";
 import { parse as parseYaml } from "yaml";
+import { OverrideMergeError, applyLayers } from "../../overrides/merge.js";
 import { ManifestParseError, parseManifest } from "../../schema/index.js";
 import { EX_NOINPUT, EX_USAGE, HarnessExitError } from "../exit-codes.js";
 import { loadManifest, resolvePaths } from "../loader.js";
 import { diffManifests, formatDiff } from "./engine.js";
-import { locateGitContext, readManifestAtRef } from "./git.js";
-function parseRefManifest(raw) {
-    let parsed;
+import { locateGitContext, readFileAtRefOrNull, readManifestAtRef, repoRelativePath, } from "./git.js";
+function parseRefYaml(raw, label) {
     try {
-        parsed = parseYaml(raw);
+        return parseYaml(raw);
     }
     catch (err) {
-        throw new HarnessExitError(`manifest at git ref is not valid YAML: ${err.message}`, EX_NOINPUT);
+        throw new HarnessExitError(`${label} is not valid YAML: ${err.message}`, EX_NOINPUT);
     }
+}
+function parseRefSchema(parsed) {
     try {
         return parseManifest(parsed);
     }
@@ -22,6 +25,73 @@ function parseRefManifest(raw) {
         throw err;
     }
 }
+/**
+ * Build the "before" manifest for `--since <ref>` with the SAME override
+ * layers the working side gets from loadManifest (task b2660f9e). Without
+ * this the ref side was override-naive while the working side was
+ * override-merged, so every override key appeared as a phantom diff.
+ *
+ * Per-layer ref semantics:
+ * - versioned in this repo and present at the ref → read at the ref
+ *   (true history of the layer);
+ * - versioned but absent at the ref → the layer was added since; the ref
+ *   side goes without it, which IS a real effective-config change;
+ * - not versioned in this repo (e.g. a ~/.harness home outside the
+ *   manifest's repo) → current content is applied to BOTH sides: the
+ *   layer is constant across the comparison and cancels out. A base
+ *   change masked by such an override does not change effective config,
+ *   so not reporting it is correct for an effective-config diff. Surfaced
+ *   via `warnings` so the operator knows the layer has no history here.
+ *
+ * Known limitation: a versioned layer REMOVED since the ref is not
+ * detected — only layers resolvable on the current filesystem are
+ * enumerated, so the removed layer's keys do not show as effective-config
+ * changes. Closing it needs at-ref layer enumeration (git ls-tree) and is
+ * consciously out of scope here.
+ */
+function buildRefManifest(ctx, since, refRaw, layerPaths, warnings) {
+    const refLayerRaws = [];
+    for (const layerPath of layerPaths) {
+        const rel = repoRelativePath(ctx, layerPath);
+        if (rel === null) {
+            warnings.push(`override layer ${layerPath} is not versioned in this repo; ` +
+                `treating its current content as constant on both sides of the comparison`);
+            let raw;
+            try {
+                raw = fs.readFileSync(layerPath, "utf8");
+            }
+            catch (err) {
+                // Mirror the working-side loader's clean failure instead of a bare
+                // Node error: resolvePaths saw the file, but it can vanish or turn
+                // unreadable between that existsSync and this read.
+                throw new HarnessExitError(`override layer could not be read: ${layerPath}: ${err.message}`, EX_NOINPUT);
+            }
+            refLayerRaws.push(parseRefYaml(raw, `override layer ${layerPath}`));
+            continue;
+        }
+        const atRef = readFileAtRefOrNull(ctx, since, rel);
+        if (atRef === null)
+            continue; // layer added since <ref>: a real change
+        refLayerRaws.push(parseRefYaml(atRef, `override layer ${rel} at git ref "${since}"`));
+    }
+    const baseRaw = parseRefYaml(refRaw, "manifest at git ref");
+    if (refLayerRaws.length === 0)
+        return parseRefSchema(baseRaw);
+    try {
+        return parseRefSchema(applyLayers(baseRaw, ...refLayerRaws));
+    }
+    catch (err) {
+        // A shape conflict between the REF-time base and a layer is a new
+        // error surface the override-naive ref path never had (e.g. the base's
+        // name-keyed list became plain since the ref). Scope the message to
+        // the ref so the operator knows it is the historical merge, not the
+        // working manifest, that failed.
+        if (err instanceof OverrideMergeError) {
+            throw new HarnessExitError(`override merge at git ref "${since}" failed: ${err.message}`, EX_NOINPUT);
+        }
+        throw err;
+    }
+}
 export function diff(opts) {
     if (!opts.since) {
         throw new HarnessExitError("harness diff requires --since <ref>; --since-apply lands in Phase 3", EX_USAGE);
@@ -29,11 +99,16 @@ export function diff(opts) {
     const resolved = resolvePaths(opts);
     const ctx = locateGitContext(resolved.base);
     const refRaw = readManifestAtRef(ctx, opts.since);
-    const before = parseRefManifest(refRaw);
+    const warnings = [];
+    const layerPaths = [
+        ...resolved.machineLayers,
+        ...(resolved.projectLayer ? [resolved.projectLayer] : []),
+    ];
+    const before = buildRefManifest(ctx, opts.since, refRaw, layerPaths, warnings);
     const { manifest: after } = loadManifest(opts);
     const changes = diffManifests(before, after);
     const output = formatDiff(changes);
-    return { changes, output, before, after };
+    return { changes, output, before, after, warnings };
 }
 export { diffManifests, formatDiff } from "./engine.js";
 //# sourceMappingURL=index.js.map

package/dist/cli/diff/index.js.map

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package/dist/cli/doctor/format.js

@@ -284,6 +284,26 @@ function formatSummary(report) {
     out.push(`  ${report.warningCount} ${warnLabel}`);
     return out;
 }
+// Grounding wiring section (task 129e1b94): rendered only when the report
+// carries a grounding section, i.e. an enabled grounding-mcp entry exists.
+// Manifests that don't use grounding stay silent, same policy as the Risk
+// Gate section above.
+function formatGroundingSection(report) {
+    const g = report.grounding;
+    if (g === undefined)
+        return [];
+    const out = ["", "Grounding"];
+    const source = g.envOverride !== null ? "operator env override" : "grounding.evidence_ledger.path";
+    out.push(`  evidence ledger: ${g.ledgerPath} (${source})`);
+    if (g.warnings.length === 0) {
+        out.push("  ✓ ledger path writable; grounding: projects EVIDENCE_LEDGER_DB onto grounding-mcp");
+    }
+    else {
+        for (const w of g.warnings)
+            out.push(`  ⚠ ${w}`);
+    }
+    return out;
+}
 export function format(report) {
     const lines = [formatHeader(report)];
     lines.push(...formatManifestSection(report));
@@ -295,6 +315,7 @@ export function format(report) {
     lines.push(...formatPolicyPacksSection(report));
     lines.push(...formatWorkflowsSection(report));
     lines.push(...formatRiskGateSection(report));
+    lines.push(...formatGroundingSection(report));
     lines.push(...formatCodexTargetSection(report));
     lines.push(...formatRogueLedgerSection(report));
     lines.push(...formatSummary(report));

package/dist/cli/doctor/format.js.map

@@ -1 +1 @@
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package/dist/cli/doctor/index.d.ts

@@ -1,4 +1,5 @@
 import { type McpProbe } from "../../probes/mcp.js";
+import { type GitIgnoreProbe } from "../validate/checks.js";
 import { type LoaderOptions } from "../loader.js";
 import { type RunCodexCheckOptions } from "./codex.js";
 import { type NpmExec } from "./npm-bin-path.js";
@@ -34,8 +35,40 @@ export interface DoctorOptions extends LoaderOptions {
      * this and the real `npm` is spawned.
      */
     npmBinExec?: NpmExec;
+    /**
+     * Test-injection knob for the solution-acceptance knob-ignored check
+     * (task 24f6ceb9). Defaults to a real `git check-ignore` probe against
+     * the process cwd; `shallow` runs degrade it to `() => null` (no spawn),
+     * mirroring how the version probe degrades. An explicit probe wins over
+     * `shallow` so tests can exercise the check without paying for spawns.
+     */
+    gitIgnoreProbe?: GitIgnoreProbe;
 }
 export { isDoctorTarget, KNOWN_DOCTOR_TARGETS };
+/**
+ * Declared-but-not-live policy pack check. `expandPolicyPacks` silently
+ * skips a pack whose `source:` token is unrecognised or whose builtin
+ * `name:` doesn't resolve in the registry — its hooks never reach
+ * `settings.json`, so the operator's gate is inert. Surface each gap
+ * as a doctor error so the misconfig is impossible to miss.
+ *
+ * Skipped (`enabled: false`) packs are NOT checked: they're not
+ * expected to be live, and flagging them would flood the report.
+ */
+/**
+ * Sentinel "cannot tell" probe: shallow runs answer every ignoredness
+ * question with `null` instead of spawning `git check-ignore`. Exported
+ * (with the resolver below) so a test can pin the no-spawn contract by
+ * identity instead of mocking `node:child_process`.
+ */
+export declare const NULL_GIT_IGNORE_PROBE: GitIgnoreProbe;
+/**
+ * Probe resolution order: an explicit (test) probe always wins; `shallow`
+ * degrades to the no-spawn sentinel, mirroring how the npm-bin probe and
+ * MCP probes degrade; otherwise the real `git check-ignore` probe runs
+ * against the process cwd.
+ */
+export declare function resolveGitIgnoreProbe(opts: Pick<DoctorOptions, "gitIgnoreProbe" | "shallow">): GitIgnoreProbe;
 export declare function doctor(opts?: DoctorOptions): Promise<DoctorReport>;
 export { format } from "./format.js";
 export type * from "./types.js";

package/dist/cli/doctor/index.js

@@ -4,12 +4,13 @@ import * as path from "node:path";
 import { compareNumericVersions } from "../../io/version-compare.js";
 import { inspectMemory } from "../../probes/memory.js";
 import { RealMcpProbe, probeAll, } from "../../probes/mcp.js";
+import { EVIDENCE_LEDGER_DB_ENV, GROUNDING_MCP_SERVER_NAME, } from "../apply/generate-settings.js";
 import { parsePackSource } from "../../policy-packs/source.js";
 import { resolveBuiltin } from "../../policy-packs/registry.js";
 import { checkPolicyPackConfigs } from "../../policy-packs/config-check.js";
 import { checkPolicyPackVersions } from "../../policy-packs/version-check.js";
 import { DEFAULT_RUNTIME } from "../../policy-packs/runtime.js";
-import { checkPolicyRiskWithoutEnvScope, checkSolutionAcceptanceProducer, } from "../validate/checks.js";
+import { checkPolicyRiskWithoutEnvScope, checkSolutionAcceptanceKnobIgnored, checkSolutionAcceptanceProducer, createDefaultGitIgnoreProbe, } from "../validate/checks.js";
 import { loadManifest } from "../loader.js";
 import { countCodexDiagnostics, runCodexTargetChecks, } from "./codex.js";
 import { checkNpmBinPath } from "./npm-bin-path.js";
@@ -338,7 +339,27 @@ function buildPolicies(manifest) {
  * Skipped (`enabled: false`) packs are NOT checked: they're not
  * expected to be live, and flagging them would flood the report.
  */
-function buildPolicyPacks(manifest, versionProbe) {
+/**
+ * Sentinel "cannot tell" probe: shallow runs answer every ignoredness
+ * question with `null` instead of spawning `git check-ignore`. Exported
+ * (with the resolver below) so a test can pin the no-spawn contract by
+ * identity instead of mocking `node:child_process`.
+ */
+export const NULL_GIT_IGNORE_PROBE = () => null;
+/**
+ * Probe resolution order: an explicit (test) probe always wins; `shallow`
+ * degrades to the no-spawn sentinel, mirroring how the npm-bin probe and
+ * MCP probes degrade; otherwise the real `git check-ignore` probe runs
+ * against the process cwd.
+ */
+export function resolveGitIgnoreProbe(opts) {
+    if (opts.gitIgnoreProbe)
+        return opts.gitIgnoreProbe;
+    if (opts.shallow)
+        return NULL_GIT_IGNORE_PROBE;
+    return createDefaultGitIgnoreProbe();
+}
+function buildPolicyPacks(manifest, versionProbe, gitIgnoreProbe) {
     const unresolved = [];
     for (const pack of manifest.policy_packs) {
         if (!pack.enabled)
@@ -374,7 +395,14 @@ function buildPolicyPacks(manifest, versionProbe) {
         actualVersion: gap.actualVersion,
         message: gap.message,
     }));
-    const solutionAcceptance = checkSolutionAcceptanceProducer(manifest);
+    // Same array as the producer check on purpose: countDiagnostics and the
+    // renderers already tally / print `solutionAcceptance` by severity, so
+    // the knob-ignored warning (task 24f6ceb9) inherits doctor parity with
+    // `harness validate` for free — the #308 pattern.
+    const solutionAcceptance = [
+        ...checkSolutionAcceptanceProducer(manifest),
+        ...checkSolutionAcceptanceKnobIgnored(manifest, gitIgnoreProbe),
+    ];
     return { unresolved, configIssues, versionGaps, solutionAcceptance };
 }
 function buildWorkflows(manifest) {
@@ -429,6 +457,60 @@ function buildRiskGate(manifest) {
     }
     return { classifiers, resolvers, whenPolicies, warnings };
 }
+/**
+ * Grounding wiring health (task 129e1b94). Only meaningful when an enabled
+ * `grounding-mcp` entry exists — callers skip the section otherwise. Checks:
+ *   1. The evidence-ledger path (the value `harness apply` projects as
+ *      `EVIDENCE_LEDGER_DB`) is writable, or creatable under its nearest
+ *      existing ancestor — an unwritable path means grounding-mcp cannot
+ *      persist evidence and every ledger-backed gate degrades.
+ *   2. An operator env override that diverges from
+ *      `grounding.evidence_ledger.path` is surfaced: the override wins at
+ *      apply time, so a stale override silently defeats the manifest value.
+ */
+function buildGrounding(manifest, server, home) {
+    const declaredPath = manifest.grounding.evidence_ledger.path;
+    const declaredExpanded = expandHome(declaredPath, home);
+    const warnings = [];
+    // Empty/whitespace "overrides" are treated as absent, matching apply's
+    // projection guard: such a value would point the ledger at "" and the
+    // projection replaces it with the manifest path anyway.
+    const rawOverride = server.env?.[EVIDENCE_LEDGER_DB_ENV];
+    const envOverride = rawOverride !== undefined && rawOverride.trim().length > 0
+        ? rawOverride
+        : null;
+    const overrideExpanded = envOverride !== null ? expandHome(envOverride, home) : null;
+    // The override is what apply preserves, so it is the EFFECTIVE path —
+    // check writability against it, not against the shadowed manifest value.
+    const ledgerPath = overrideExpanded ?? declaredExpanded;
+    if (overrideExpanded !== null && overrideExpanded !== declaredExpanded) {
+        warnings.push(`tools.mcp.grounding-mcp.env.${EVIDENCE_LEDGER_DB_ENV} ("${envOverride}") ` +
+            `overrides grounding.evidence_ledger.path ("${declaredPath}"); the env wins at apply, ` +
+            `so align the two or drop the env so the manifest value applies`);
+    }
+    let ledgerPathWritable = true;
+    try {
+        if (fs.existsSync(ledgerPath)) {
+            fs.accessSync(ledgerPath, fs.constants.W_OK);
+        }
+        else {
+            let dir = path.dirname(ledgerPath);
+            while (!fs.existsSync(dir)) {
+                const parent = path.dirname(dir);
+                if (parent === dir)
+                    break;
+                dir = parent;
+            }
+            fs.accessSync(dir, fs.constants.W_OK);
+        }
+    }
+    catch {
+        ledgerPathWritable = false;
+        warnings.push(`evidence-ledger path ${ledgerPath} is not writable (and not creatable) — ` +
+            `grounding-mcp cannot persist evidence, so ledger-backed gates degrade to warn`);
+    }
+    return { ledgerPath, ledgerPathWritable, envOverride, warnings };
+}
 function manifestSection(manifest) {
     const topLevelKeys = [
         "grounding",
@@ -501,6 +583,9 @@ function countDiagnostics(report) {
             warningCount++;
     }
     warningCount += report.riskGate.warnings.length;
+    if (report.grounding !== undefined) {
+        warningCount += report.grounding.warnings.length;
+    }
     if (report.npmGlobalBin?.status === "warn")
         warningCount++;
     if (report.memory.routerExecutable && !report.memory.routerExecutable.exists)
@@ -563,9 +648,13 @@ export async function doctor(opts = {}) {
     const hooks = checkHooks(manifest, home, opts);
     const policies = buildPolicies(manifest);
     const policyPacksVersionProbe = opts.versionProbe ?? (() => null);
-    const policyPacks = buildPolicyPacks(manifest, policyPacksVersionProbe);
+    const policyPacks = buildPolicyPacks(manifest, policyPacksVersionProbe, resolveGitIgnoreProbe(opts));
     const workflows = buildWorkflows(manifest);
     const riskGate = buildRiskGate(manifest);
+    const groundingServer = manifest.tools.mcp.find((m) => m.name === GROUNDING_MCP_SERVER_NAME && m.enabled !== false) ?? null;
+    const grounding = groundingServer !== null
+        ? buildGrounding(manifest, groundingServer, home)
+        : undefined;
     const manifestSec = manifestSection(manifest);
     const rogueLedgerDbs = scanForRogueLedgers({
         homeDir: opts.rogueLedgerScanOptions?.homeDir ?? home,
@@ -596,6 +685,7 @@ export async function doctor(opts = {}) {
         policyPacks,
         workflows,
         riskGate,
+        ...(grounding !== undefined ? { grounding } : {}),
         rogueLedgerDbs,
         ...(npmGlobalBin !== undefined ? { npmGlobalBin } : {}),
     };