@opengsd/gsd-core 1.5.0-rc.3 → 1.5.0-rc.4

package/gsd-core/bin/lib/capability-writer.cjs

@@ -0,0 +1,354 @@
+"use strict";
+/**
+ * Capability Writer — ADR-1213 write-side inverse of capability-state resolver.
+ *
+ * Exports:
+ *   setCapabilityState(cwd, runtimeConfigDir, desired, opts?)
+ *     → { capabilities: CapabilityStateEntry[], warnings: string[] }
+ *   cmdCapabilitySet(cwd, runtimeConfigDir, capId, options, raw)
+ *
+ * Projection rules (three axes: install, surface, config):
+ *   - enabled axis: mutates .gsd-surface.json via readSurface/writeSurface
+ *   - gates axis: mutates .planning/config.json via setConfigValues (batched)
+ *   - materialize: optionally calls applySurface to write skill files
+ *   - re-resolve: always calls resolveCapabilityRuntimeState for the return value
+ *
+ * Dependencies (leaf modules only — no circular risk):
+ *   - ./core.cjs               (output, error)
+ *   - ./capability-state.cjs   (resolveCapabilityRuntimeState, _resolveManifest, _resolveCommandsGsdDir)
+ *   - ./surface.cjs            (readSurface, writeSurface, applySurface)
+ *   - ./install-profiles.cjs   (readActiveProfile)
+ *   - ./config.cjs             (setConfigValues)
+ *   - ./runtime-artifact-layout.cjs (resolveRuntimeArtifactLayout)
+ *   - capability-registry.cjs  (loaded at call time)
+ */
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const core = require("./core.cjs");
+const { output: coreOutput, error: coreError } = core;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const capabilityStateMod = require("./capability-state.cjs");
+const { resolveCapabilityRuntimeState, _resolveManifest, _resolveCommandsGsdDir } = capabilityStateMod;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const surfaceMod = require("./surface.cjs");
+const { readSurface, writeSurface, applySurface } = surfaceMod;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const installProfilesMod = require("./install-profiles.cjs");
+const { readActiveProfile } = installProfilesMod;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const configMod = require("./config.cjs");
+const { setConfigValues } = configMod;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const planningWorkspaceMod = require("./planning-workspace.cjs");
+const { planningDir } = planningWorkspaceMod;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const nodefs = require("fs");
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const nodepath = require("path");
+// ─── Implementation ───────────────────────────────────────────────────────────
+/**
+ * Write-side capability state mutator.
+ *
+ * Applies desired capability state changes (enabled axis via surface, gates
+ * axis via config) then re-resolves and returns the full capability state.
+ *
+ * Control flow:
+ *   1. RESOLVE BEFORE STATE: call resolveCapabilityRuntimeState once to get the
+ *      canonical runtimeConfigDir and current capability state.
+ *   2. VALIDATION PASS (no writes): validate each desired entry against the
+ *      registry and `before` state; collect errors and warnings.
+ *   3. If errors → return early with before.capabilities (no writes performed).
+ *   4. APPLY PASS: compute new surface state, writeSurface once if changed,
+ *      setConfigValues once for gate writes; materialize if opts provided.
+ *   5. RE-RESOLVE: call resolveCapabilityRuntimeState again to get final state.
+ *   6. POST CHECKS: enabled=true but not-surfaced (not-in-profile) error;
+ *      present-but-dead warning; append resolver warnings.
+ *   7. Return { capabilities: after.capabilities, warnings, errors }.
+ */
+function setCapabilityState(cwd, runtimeConfigDir, desired, opts) {
+    const warnings = [];
+    const errors = [];
+    // ── Step 1: Resolve BEFORE state once ────────────────────────────────────
+    const before = resolveCapabilityRuntimeState(cwd, runtimeConfigDir);
+    const resolvedConfigDir = before.runtimeConfigDir;
+    // ── Load registry ─────────────────────────────────────────────────────────
+    const registry = before.registry;
+    const capabilitiesMap = (registry['capabilities'] && typeof registry['capabilities'] === 'object' && !Array.isArray(registry['capabilities'])
+        ? registry['capabilities']
+        : {});
+    // ── Step 2: VALIDATION PASS (no writes) ──────────────────────────────────
+    // Accumulate all valid gate writes and surface deltas.
+    // If ANY error is found, we will return early without writing anything.
+    const pendingGateWrites = [];
+    // surface-delta accumulators: ids to add to / remove from disabledClusters
+    const idsToDisable = [];
+    const idsToEnable = [];
+    // Track which ids need surface loading (have skills + explicit enabled flag)
+    let needsSurface = false;
+    for (const entry of desired) {
+        const { id, enabled, gates } = entry;
+        // Validate capability id
+        if (!Object.prototype.hasOwnProperty.call(capabilitiesMap, id)) {
+            errors.push(`unknown capability: "${id}"`);
+            continue;
+        }
+        const capObj = capabilitiesMap[id];
+        const skillsRaw = capObj['skills'];
+        const skills = Array.isArray(skillsRaw)
+            ? skillsRaw.filter((s) => typeof s === 'string')
+            : [];
+        const configDef = (capObj['config'] && typeof capObj['config'] === 'object' && !Array.isArray(capObj['config'])
+            ? capObj['config']
+            : {});
+        // ── Validate gate keys / values ──────────────────────────────────────────
+        if (gates !== undefined) {
+            for (const [key, val] of Object.entries(gates)) {
+                if (!Object.prototype.hasOwnProperty.call(configDef, key)) {
+                    errors.push(`unknown gate key "${key}" for capability "${id}"`);
+                    continue;
+                }
+                if (typeof val !== 'boolean') {
+                    errors.push(`gate value for "${key}" must be boolean, got ${typeof val}`);
+                    continue;
+                }
+                pendingGateWrites.push({ keyPath: key, value: val });
+            }
+        }
+        // ── Validate enabled axis ────────────────────────────────────────────────
+        if (enabled !== undefined) {
+            if (skills.length === 0) {
+                // Advisory only — no surface effect possible
+                warnings.push(`capability "${id}" owns no skills; 'enabled' has no surface effect — use gates to toggle its hooks`);
+                continue;
+            }
+            // Install-floor check: cannot enable a capability whose skills are not installed
+            if (enabled === true) {
+                const beforeEntry = before.capabilities.find((c) => c.id === id);
+                if (beforeEntry && beforeEntry.installed === false) {
+                    errors.push(`cannot enable "${id}": its skills are not in the install profile`);
+                    continue;
+                }
+            }
+            needsSurface = true;
+            if (enabled === false) {
+                idsToDisable.push(id);
+            }
+            else {
+                idsToEnable.push(id);
+            }
+        }
+    }
+    // ── Fix D: Pre-validate config.json parseability before any write ────────
+    // If there are pending gate writes, attempt to read and parse the target
+    // config.json BEFORE writing anything. A malformed file would cause
+    // setConfigValues to error() mid-operation leaving a partial write.
+    if (pendingGateWrites.length > 0) {
+        try {
+            const configJsonPath = nodepath.join(planningDir(cwd), 'config.json');
+            if (nodefs.existsSync(configJsonPath)) {
+                const raw = nodefs.readFileSync(configJsonPath, 'utf-8');
+                try {
+                    JSON.parse(raw);
+                }
+                catch (parseErr) {
+                    const msg = parseErr instanceof Error ? parseErr.message : String(parseErr);
+                    errors.push(`config.json is malformed: ${msg}`);
+                }
+            }
+        }
+        catch {
+            // Cannot read the file path — not an error (e.g. planningDir env-var issue); let setConfigValues handle it
+        }
+    }
+    // ── Step 3: Early return on validation errors ────────────────────────────
+    if (errors.length > 0) {
+        return {
+            capabilities: before.capabilities,
+            warnings,
+            errors,
+        };
+    }
+    // ── Step 4: APPLY PASS ────────────────────────────────────────────────────
+    // ── Surface writes ────────────────────────────────────────────────────────
+    if (needsSurface && (idsToDisable.length > 0 || idsToEnable.length > 0)) {
+        const existing = readSurface(resolvedConfigDir);
+        let pendingSurface = existing ?? {
+            baseProfile: readActiveProfile(resolvedConfigDir) ?? 'full',
+            disabledClusters: [],
+            explicitAdds: [],
+            explicitRemoves: [],
+        };
+        let surfaceChanged = false;
+        for (const id of idsToDisable) {
+            // Add id to disabledClusters (dedupe)
+            if (!pendingSurface.disabledClusters.includes(id)) {
+                pendingSurface = {
+                    ...pendingSurface,
+                    disabledClusters: [...pendingSurface.disabledClusters, id],
+                };
+                surfaceChanged = true;
+            }
+            // Fix A: explicitAdds contains SKILL STEMS, not capability ids.
+            // Remove the capability's skill stems from explicitAdds so that
+            // resolveSurface does not re-add those skills after the cluster disable.
+            const capObjForDisable = capabilitiesMap[id];
+            const skillsRawForDisable = capObjForDisable?.['skills'];
+            const skillStemsForDisable = Array.isArray(skillsRawForDisable)
+                ? skillsRawForDisable.filter((s) => typeof s === 'string')
+                : [];
+            const newExplicitAdds = pendingSurface.explicitAdds.filter((x) => !skillStemsForDisable.includes(x));
+            if (newExplicitAdds.length !== pendingSurface.explicitAdds.length) {
+                pendingSurface = { ...pendingSurface, explicitAdds: newExplicitAdds };
+                surfaceChanged = true;
+            }
+        }
+        for (const id of idsToEnable) {
+            // Remove id from disabledClusters
+            if (pendingSurface.disabledClusters.includes(id)) {
+                pendingSurface = {
+                    ...pendingSurface,
+                    disabledClusters: pendingSurface.disabledClusters.filter((x) => x !== id),
+                };
+                surfaceChanged = true;
+            }
+            // Fix A (enable branch): also remove the capability's skill stems from
+            // explicitRemoves so that resolveSurface does not subtract those skills.
+            // Do NOT add anything to explicitAdds — a cap that was only in explicitAdds
+            // and was disabled is caught by the post-check below.
+            const capObjForEnable = capabilitiesMap[id];
+            const skillsRawForEnable = capObjForEnable?.['skills'];
+            const skillStemsForEnable = Array.isArray(skillsRawForEnable)
+                ? skillsRawForEnable.filter((s) => typeof s === 'string')
+                : [];
+            const newExplicitRemoves = pendingSurface.explicitRemoves.filter((x) => !skillStemsForEnable.includes(x));
+            if (newExplicitRemoves.length !== pendingSurface.explicitRemoves.length) {
+                pendingSurface = { ...pendingSurface, explicitRemoves: newExplicitRemoves };
+                surfaceChanged = true;
+            }
+        }
+        if (surfaceChanged) {
+            writeSurface(resolvedConfigDir, pendingSurface);
+        }
+    }
+    // ── Config writes (once, batched) ─────────────────────────────────────────
+    if (pendingGateWrites.length > 0) {
+        setConfigValues(cwd, pendingGateWrites);
+    }
+    // ── Materialize (optional) ────────────────────────────────────────────────
+    if (opts?.materialize) {
+        const { runtime, scope } = opts.materialize;
+        try {
+            // eslint-disable-next-line @typescript-eslint/no-require-imports
+            const runtimeArtifactLayout = require('./runtime-artifact-layout.cjs');
+            // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+            const layout = runtimeArtifactLayout.resolveRuntimeArtifactLayout(runtime, resolvedConfigDir, scope);
+            const commandsGsdDir = _resolveCommandsGsdDir();
+            const manifest = _resolveManifest(commandsGsdDir, resolvedConfigDir);
+            // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+            applySurface(resolvedConfigDir, layout, manifest, undefined, registry);
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            // Fix C: materialise was explicitly requested — a failure is an error (non-zero exit),
+            // not merely advisory.
+            errors.push(`materialize failed: ${msg}`);
+        }
+    }
+    // ── Step 5: RE-RESOLVE ────────────────────────────────────────────────────
+    const after = resolveCapabilityRuntimeState(cwd, resolvedConfigDir);
+    // ── Step 6: POST CHECKS ───────────────────────────────────────────────────
+    // Check: desired enabled=true but not actually enabled after write
+    // (catches the not-in-profile / not-surfaced silent no-op case).
+    // The install-floor case (installed===false) was already caught in validation.
+    for (const entry of desired) {
+        if (entry.enabled === true) {
+            const afterCap = after.capabilities.find((c) => c.id === entry.id);
+            if (afterCap && afterCap.enabled !== true) {
+                errors.push(`cannot enable "${entry.id}": not in the active surface/profile (widen the profile or use /gsd:surface enable)`);
+            }
+        }
+        // Fix B: desired enabled=false — assert it is actually disabled after write.
+        // Prevents "off means off" silent failures (e.g. explicitAdds containing the
+        // cap's skill stems re-adds them after the cluster disable).
+        if (entry.enabled === false) {
+            const afterCap = after.capabilities.find((c) => c.id === entry.id);
+            if (afterCap && afterCap.enabled !== false) {
+                errors.push(`failed to disable "${entry.id}": still surfaced after write`);
+            }
+        }
+    }
+    // Check: present-but-dead — SCOPED to touched (desired) capabilities only.
+    const desiredIds = new Set(desired.map((d) => d.id));
+    for (const cap of after.capabilities) {
+        if (!desiredIds.has(cap.id))
+            continue;
+        if (cap.enabled === true &&
+            cap.hooks.length > 0 &&
+            cap.hooks.every((h) => !h.configured)) {
+            warnings.push(`capability "${cap.id}" is surfaced but every hook is gated off — did you mean enabled:false?`);
+        }
+    }
+    // Append resolver's own warnings
+    for (const w of after.warnings) {
+        warnings.push(w);
+    }
+    return {
+        capabilities: after.capabilities,
+        warnings,
+        errors,
+    };
+}
+/**
+ * CLI command entry point for `gsd-tools capability set`.
+ *
+ * Builds one DesiredCapability from the provided options, calls setCapabilityState,
+ * then prints the result. When raw=true emits JSON; else emits a human summary.
+ * Warnings are always printed to stderr.
+ */
+function cmdCapabilitySet(cwd, runtimeConfigDir, capId, options, raw) {
+    const desired = [
+        {
+            id: capId,
+            ...(options.enabled !== undefined ? { enabled: options.enabled } : {}),
+            ...(options.gates ? { gates: options.gates } : {}),
+        },
+    ];
+    const opts = options.runtime
+        ? { materialize: { runtime: options.runtime, scope: options.scope ?? 'global' } }
+        : undefined;
+    const result = setCapabilityState(cwd, runtimeConfigDir, desired, opts);
+    if (raw) {
+        // Raw mode: emit JSON to stdout including errors; exit non-zero if errors present.
+        // Do NOT print human stderr lines — raw consumers parse the JSON.
+        coreOutput({ capabilities: result.capabilities, warnings: result.warnings, errors: result.errors }, true);
+        if (result.errors.length > 0) {
+            process.exit(1);
+        }
+        return;
+    }
+    // Human mode: print warnings and errors to stderr (non-fatally for warnings).
+    for (const w of result.warnings) {
+        process.stderr.write(`capability set: warning: ${w}\n`);
+    }
+    for (const e of result.errors) {
+        process.stderr.write(`capability set: error: ${e}\n`);
+    }
+    // Exit non-zero if any errors (hard failures — requested action was not realized).
+    if (result.errors.length > 0) {
+        coreError(`capability set: ${String(result.errors.length)} error(s) — see above`);
+        return; // unreachable — coreError calls process.exit(1)
+    }
+    // Human-readable summary: focus on the target capability
+    const cap = result.capabilities.find((c) => c.id === capId);
+    if (!cap) {
+        const msg = `capability "${capId}" not found in registry`;
+        coreOutput(msg, false, msg);
+        return;
+    }
+    const activeHooks = cap.hooks.filter((h) => h.active).length;
+    const summary = `capability ${capId}: enabled=${String(cap.enabled)}, surfaced=${String(cap.surfaced)}, installed=${String(cap.installed)}, activeHooks=${String(activeHooks)}/${String(cap.hooks.length)}`;
+    coreOutput({ id: cap.id, enabled: cap.enabled, surfaced: cap.surfaced, installed: cap.installed, warnings: result.warnings.length > 0 ? result.warnings : undefined }, false, summary);
+}
+module.exports = {
+    setCapabilityState,
+    cmdCapabilitySet,
+};

package/gsd-core/bin/lib/config.cjs

@@ -368,6 +368,42 @@ function cmdConfigEnsureSection(cwd, raw) {
         output(ensureConfigFileResult, raw, 'exists');
     }
 }
+/**
+ * Shared helper: write a single key-path into an in-memory config object.
+ *
+ * Prototype-pollution guard: reject dangerous segments via inline literal
+ * comparisons on the exact key used to index `current`, immediately before
+ * each write. The inline comparison is the barrier CodeQL's
+ * js/prototype-pollution-utility query recognises — the previous Set-based
+ * pre-loop check was functionally correct but not traced through, so
+ * code-scanning alert #26 kept firing. Behaviour is unchanged from #663.
+ *
+ * Returns the previous value at the leaf key (undefined if absent).
+ * Never writes to disk — callers handle persistence.
+ * Calls error() (process.exit(1)) on prototype-pollution attempts.
+ */
+function _setNestedValue(config, keyPath, parsedValue) {
+    const keys = keyPath.split('.');
+    let current = config;
+    for (let i = 0; i < keys.length - 1; i++) {
+        const key = keys[i];
+        if (key === '__proto__' || key === 'prototype' || key === 'constructor') {
+            error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
+        }
+        const existingChild = current[key];
+        if (existingChild === undefined || existingChild === null || typeof existingChild !== 'object' || Array.isArray(existingChild)) {
+            current[key] = {};
+        }
+        current = current[key];
+    }
+    const lastKey = keys[keys.length - 1];
+    if (lastKey === '__proto__' || lastKey === 'prototype' || lastKey === 'constructor') {
+        error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
+    }
+    const previousValue = current[lastKey];
+    current[lastKey] = parsedValue;
+    return previousValue;
+}
 /**
  * Sets a value in the config file, allowing nested values via dot notation (e.g.,
  * "workflow.research").
@@ -388,35 +424,52 @@ function setConfigValue(cwd, keyPath, parsedValue) {
         catch (err) {
             error('Failed to read config.json: ' + err.message, ERROR_REASON.CONFIG_PARSE_FAILED);
         }
-        // Set nested value using dot notation (e.g., "workflow.research").
-        // Prototype-pollution guard: reject dangerous segments via inline literal
-        // comparisons on the exact key used to index `current`, immediately before
-        // each write. The inline comparison is the barrier CodeQL's
-        // js/prototype-pollution-utility query recognises — the previous Set-based
-        // pre-loop check was functionally correct but not traced through, so
-        // code-scanning alert #26 kept firing. Behaviour is unchanged from #663.
-        const keys = keyPath.split('.');
-        let current = config;
-        for (let i = 0; i < keys.length - 1; i++) {
-            const key = keys[i];
-            if (key === '__proto__' || key === 'prototype' || key === 'constructor') {
-                error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
-            }
-            if (current[key] === undefined || typeof current[key] !== 'object') {
-                current[key] = {};
+        const previousValue = _setNestedValue(config, keyPath, parsedValue);
+        // Write back
+        try {
+            (0, shell_command_projection_cjs_1.platformWriteSync)(configPath, JSON.stringify(config, null, 2));
+            return { updated: true, key: keyPath, value: parsedValue, previousValue };
+        }
+        catch (err) {
+            error('Failed to write config.json: ' + err.message);
+        }
+    });
+}
+/**
+ * Batched sibling of setConfigValue: apply multiple key-path writes in a
+ * single load → set-all → write cycle inside ONE withPlanningLock call.
+ *
+ * Returns { updated: true, results: SetConfigValueResult[] } on success.
+ * An empty entries array is a no-op and returns { updated: false, results: [] }.
+ *
+ * Prototype-pollution guards are enforced per entry (identical inline-literal
+ * guards as setConfigValue — CodeQL barrier requirement).
+ */
+function setConfigValues(cwd, entries) {
+    if (entries.length === 0) {
+        return { updated: false, results: [] };
+    }
+    const configPath = node_path_1.default.join(planningDir(cwd), 'config.json');
+    return withPlanningLock(cwd, () => {
+        // Load existing config or start with empty object
+        let config = {};
+        try {
+            if (node_fs_1.default.existsSync(configPath)) {
+                config = JSON.parse(node_fs_1.default.readFileSync(configPath, 'utf-8'));
             }
-            current = current[key];
         }
-        const lastKey = keys[keys.length - 1];
-        if (lastKey === '__proto__' || lastKey === 'prototype' || lastKey === 'constructor') {
-            error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
+        catch (err) {
+            error('Failed to read config.json: ' + err.message, ERROR_REASON.CONFIG_PARSE_FAILED);
         }
-        const previousValue = current[lastKey]; // Capture previous value before overwriting
-        current[lastKey] = parsedValue;
-        // Write back
+        const results = [];
+        for (const entry of entries) {
+            const previousValue = _setNestedValue(config, entry.keyPath, entry.value);
+            results.push({ updated: true, key: entry.keyPath, value: entry.value, previousValue });
+        }
+        // Write back once for all entries
         try {
             (0, shell_command_projection_cjs_1.platformWriteSync)(configPath, JSON.stringify(config, null, 2));
-            return { updated: true, key: keyPath, value: parsedValue, previousValue };
+            return { updated: true, results };
         }
         catch (err) {
             error('Failed to write config.json: ' + err.message);
@@ -734,4 +787,7 @@ module.exports = {
     cmdConfigNewProject,
     cmdConfigPath,
     cmdMigrateConfig,
+    // Exported for programmatic use by capability-writer and tests
+    setConfigValue,
+    setConfigValues,
 };

package/gsd-core/bin/lib/edge-probe.cjs

@@ -19,7 +19,7 @@
  * edges, and (via probe-core) merges author resolutions into a coverage report.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.EDGE_VALIDATORS = exports.TAXONOMY = exports.VALID_SHAPES = exports.SHAPE_CUES = void 0;
+exports.EDGE_VALIDATORS = exports.UNCLASSIFIED_CATEGORY = exports.TAXONOMY = exports.VALID_SHAPES = exports.SHAPE_CUES = void 0;
 exports.classifyShape = classifyShape;
 exports.applicableCategories = applicableCategories;
 exports.validateRequirement = validateRequirement;
@@ -74,8 +74,15 @@ function applicableCategories(shapes) {
  * taxonomy; both verification tiers require a non-empty `resolution` (an explicit AC's text
  * or a backstop note) so plan-phase has a criterion to lift.
  */
+/**
+ * Pseudo-category for a requirement whose prose matched NO shape cue (#1110). It is a soft
+ * "review manually" signal, NOT a 9th taxonomy category: it stays out of `TAXONOMY` (the closed
+ * eight) and only joins `EDGE_VALIDATORS.categories` so `analyzeCoverage` accepts the item.
+ */
+exports.UNCLASSIFIED_CATEGORY = 'unclassified';
+const UNCLASSIFIED_PROBE = 'unclassified — review manually';
 exports.EDGE_VALIDATORS = {
-    categories: exports.TAXONOMY.map((c) => c.id),
+    categories: [...exports.TAXONOMY.map((c) => c.id), exports.UNCLASSIFIED_CATEGORY],
     verification: ['explicit', 'backstop'],
     requiredFieldsByVerification: { explicit: ['resolution'], backstop: ['resolution'] },
 };
@@ -126,6 +133,22 @@ function proposeEdges(requirement) {
     }
     else {
         shapes = classifyShape(requirement.text);
+        if (shapes.length === 0) {
+            // Prose present but no shape cue matched. Do NOT silently drop it (#1110): an
+            // edge-relevant requirement whose phrasing missed every cue would otherwise vanish from
+            // coverage with no signal — the exact blind spot this probe exists to catch. Surface ONE
+            // soft, dismissible "unclassified — review manually" candidate. The explicit `shapes: []`
+            // opt-out (handled above) stays silent — that is the author's deliberate "no edge surface".
+            return [{
+                    requirement_id: requirement.id,
+                    category: exports.UNCLASSIFIED_CATEGORY,
+                    status: 'unresolved',
+                    verification: null,
+                    resolution: null,
+                    reason: null,
+                    probe: UNCLASSIFIED_PROBE,
+                }];
+        }
     }
     return applicableCategories(shapes).map((catId) => {
         const cat = exports.TAXONOMY.find((c) => c.id === catId);

package/gsd-core/bin/lib/frontmatter.cjs

@@ -202,13 +202,60 @@ function reconstructFrontmatter(obj) {
     return lines.join('\n');
 }
 function spliceFrontmatter(content, newObj) {
-    const yamlStr = reconstructFrontmatter(newObj);
     const match = content.match(/^---\r?\n[\s\S]+?\r?\n---/);
     if (match) {
+        // Identity-preservation (additive, lossless round-trip): `reconstructFrontmatter` is a
+        // deliberately lossy serializer — it cannot faithfully re-emit nested object-list items
+        // (e.g. must_haves.artifacts / must_haves.prohibitions, whose items are `{ path, provides }`
+        // / `{ statement, status, … }` maps). When the caller is writing back a value that is
+        // STRUCTURALLY UNCHANGED from the original parse (the canonical CRUD round-trip and the
+        // #644 prohibition schema round-trip both do this), regenerating from the lossy object would
+        // silently mangle those blocks. Detect that case by deep-equality against a re-parse of the
+        // original frontmatter and preserve the ORIGINAL raw text verbatim — a true no-op splice.
+        // This touches neither the parser (`extractFrontmatter`) nor `parseMustHavesBlock`; it only
+        // makes the existing splice faithful when nothing changed. A genuine mutation (different
+        // object) still flows through `reconstructFrontmatter` exactly as before.
+        try {
+            if (frontmatterDeepEqual(extractFrontmatter(content), newObj)) {
+                return content;
+            }
+        }
+        catch {
+            /* fall through to regeneration on any comparison hiccup */
+        }
+        const yamlStr = reconstructFrontmatter(newObj);
         return `---\n${yamlStr}\n---` + content.slice(match[0].length);
     }
+    const yamlStr = reconstructFrontmatter(newObj);
     return `---\n${yamlStr}\n---\n\n` + content;
 }
+/**
+ * Structural deep-equality for two parsed frontmatter objects. Order-sensitive for arrays
+ * (YAML lists are ordered), key-order-insensitive for objects. Used only by `spliceFrontmatter`
+ * to recognize a no-op write-back; intentionally narrow (handles the string / string[] /
+ * nested-object shapes `extractFrontmatter` produces).
+ */
+function frontmatterDeepEqual(a, b) {
+    if (a === b)
+        return true;
+    if (a == null || b == null)
+        return a === b;
+    if (Array.isArray(a) || Array.isArray(b)) {
+        if (!Array.isArray(a) || !Array.isArray(b) || a.length !== b.length)
+            return false;
+        return a.every((v, i) => frontmatterDeepEqual(v, b[i]));
+    }
+    if (typeof a === 'object' && typeof b === 'object') {
+        const ao = a;
+        const bo = b;
+        const ak = Object.keys(ao);
+        const bk = Object.keys(bo);
+        if (ak.length !== bk.length)
+            return false;
+        return ak.every((k) => Object.prototype.hasOwnProperty.call(bo, k) && frontmatterDeepEqual(ao[k], bo[k]));
+    }
+    return false;
+}
 function parseMustHavesBlock(content, blockName) {
     // Extract a specific block from must_haves in raw frontmatter YAML
     // Handles 3-level nesting: must_haves > artifacts/key_links > [{path, provides, ...}]
@@ -431,6 +478,11 @@ function cmdFrontmatterValidate(cwd, filePath, schemaName, raw) {
 }
 module.exports = {
     extractFrontmatter,
+    // Additive alias (#644 prohibition-probe schema contract): the probe round-trip seam reads a
+    // frontmatter object via `parseFrontmatter` (the name the contract test pins). It is the SAME
+    // function as `extractFrontmatter` — a bare-object parse with no behavior change — exposed under
+    // the alias so the prohibition schema round-trip and any future caller can use the canonical name.
+    parseFrontmatter: extractFrontmatter,
     reconstructFrontmatter,
     spliceFrontmatter,
     parseMustHavesBlock,