Merge branch 'next' into fix/2028-phase-complete-milestone-end-and-workstream-guard

.changeset/2043-phase-token-single-digit-slug.md

@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 2059
+---
+**Phase directories whose slug begins with a single digit now resolve correctly.** A phase like `46-6-rs-pipeline-orchestrator` (roadmap name "6 Rs Pipeline Orchestrator") had its phase token over-collected as `46-6` instead of `46`, so `gsd-tools` phase-by-number lookups resolved `phase_dir=null` / `has_context=false` (breaking `init.plan-phase`, `init.phase-op`, and downstream execute/verify/ship). Numeric phase-token components must now be zero-padded (≥2 digits), so a single-digit slug word is no longer absorbed into the token. Fixed consistently across every same-class implementation — `extractPhaseToken`, `PHASE_TOKEN_FROM_DIR_RE` and `canonicalPlanStem` (health checks / plan pairing), `isDirInMilestone`'s numeric matcher (milestone filtering), and `extractCanonicalPlanId` — so the health-check and milestone-filter subsystems are fixed alongside phase resolution.

.changeset/2046-config-set-null-unset.md

@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 2058
+---
+**`gsd-tools config-set <key> null` now clears (removes) the key instead of persisting the literal string `"null"`.** The documented "Clear" action previously fell through the value parser and stored `"null"` — a truthy value — so "cleared" keys stayed set and `config-get` returned `"null"`; for secret keys (`brave_search`/`firecrawl`/`exa_search`) a masked success line hid a truthy value on disk that integrations could pass along as a real credential. `config-set <key> null` now deletes the key (short-circuiting the typed per-key validators so clearing an enum/boolean/number key removes it rather than being rejected), making the "Clear" flows in `settings-integrations.md` / `settings-advanced.md` actually clear.

src/config.cts

@@ -38,6 +38,14 @@ interface SetConfigValueResult {
   previousValue: unknown;
 }
 
+interface UnsetConfigValueResult {
+  updated: boolean;
+  unset: true;
+  key: string;
+  value: null;
+  previousValue: unknown;
+}
+
 interface WorkstreamContext {
   configPath?: string;
   [key: string]: unknown;
@@ -452,6 +460,87 @@ function _setNestedValue(
   return previousValue;
 }
 
+/**
+ * Deletes a value from the config object, allowing nested values via dot
+ * notation (e.g., "review.models.gemini"). Mirrors `_setNestedValue`'s
+ * prototype-pollution guard on every path segment (including intermediates).
+ *
+ * Unlike `_setNestedValue`, this NEVER creates missing intermediate objects —
+ * if any segment along the path is missing (or not a plain, non-array
+ * object), the key doesn't exist and we return early without mutating
+ * `config` at all.
+ *
+ * Does not prune now-empty parent objects after deletion (matches the
+ * conservative, structure-preserving behaviour callers expect from a bare
+ * unset).
+ *
+ * Returns { previousValue, existed } — existed is false when the leaf key
+ * (or an intermediate segment) was never present.
+ * Calls error() (process.exit(1)) on prototype-pollution attempts.
+ */
+function _unsetNestedValue(
+  config: Record<string, unknown>,
+  keyPath: string,
+): { previousValue: unknown; existed: boolean } {
+  const keys = keyPath.split('.');
+  let current: Record<string, unknown> = 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)) {
+      // Path doesn't exist — nothing to unset, and we must not create it.
+      return { previousValue: undefined, existed: false };
+    }
+    current = existingChild as Record<string, unknown>;
+  }
+  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 existed = Object.prototype.hasOwnProperty.call(current, lastKey);
+  const previousValue = current[lastKey];
+  if (existed) {
+    delete current[lastKey];
+  }
+  return { previousValue, existed };
+}
+
+/**
+ * Deletes a key from the config file, allowing nested values via dot
+ * notation. Mirrors `setConfigValue`'s load/lock/write cycle.
+ *
+ * Does not call `output()`, so can be used as one step in a command without triggering `exit(0)` in
+ * the happy path. But note that `error()` will still `exit(1)` out of the process.
+ */
+function unsetConfigValue(cwd: string, keyPath: string): UnsetConfigValueResult {
+  const configPath = path.join(planningDir(cwd), 'config.json');
+
+  return withPlanningLock(cwd, () => {
+    // Load existing config or start with empty object
+    let config: Record<string, unknown> = {};
+    try {
+      if (fs.existsSync(configPath)) {
+        config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;
+      }
+    } catch (err) {
+      error('Failed to read config.json: ' + (err as Error).message, ERROR_REASON.CONFIG_PARSE_FAILED);
+    }
+
+    const { previousValue, existed } = _unsetNestedValue(config, keyPath);
+
+    // Write back
+    try {
+      platformWriteSync(configPath, JSON.stringify(config, null, 2));
+      return { updated: existed, unset: true, key: keyPath, value: null, previousValue };
+    } catch (err) {
+      error('Failed to write config.json: ' + (err as Error).message);
+    }
+  }) as UnsetConfigValueResult;
+}
+
 /**
  * Sets a value in the config file, allowing nested values via dot notation (e.g.,
  * "workflow.research").
@@ -586,6 +675,7 @@ function cmdConfigSet(cwd: string, keyPath: string | undefined, value: string |
   let parsedValue: unknown = val;
   if (val === 'true') parsedValue = true;
   else if (val === 'false') parsedValue = false;
+  else if (val === 'null') parsedValue = null;
   // #1581: Number.isFinite (not !isNaN) so 'Infinity'/'-Infinity' are NOT
   // coerced to non-finite numbers that JSON.stringify later renders as `null`
   // (disk=null while the CLI echoed 'Infinity'). They fall through to the
@@ -596,6 +686,25 @@ function cmdConfigSet(cwd: string, keyPath: string | undefined, value: string |
     try { parsedValue = JSON.parse(val); } catch { /* keep as string */ }
   }
 
+  // #2046: a bare `null` unsets (deletes) the key — the documented "Clear" action.
+  // Short-circuits before every typed per-key validator so clearing a typed key
+  // (enum/boolean/number) removes it rather than being rejected. Deleting (not
+  // persisting JSON null) is the correct "clear": a persisted null is still a
+  // present, truthy-adjacent value that consumers must special-case — worst for
+  // secret keys where a leftover value can be passed as a real credential.
+  if (parsedValue === null) {
+    const unsetResult = unsetConfigValue(cwd, kp);
+    if (isSecretKey(kp)) {
+      const maskedPrev = unsetResult.previousValue === undefined
+        ? undefined
+        : maskSecret(unsetResult.previousValue as Parameters<typeof maskSecret>[0]);
+      output({ ...unsetResult, value: null, previousValue: maskedPrev, masked: true }, raw, `${kp} unset`);
+      return;
+    }
+    output(unsetResult, raw, `${kp} unset`);
+    return;
+  }
+
   // #1581: project_code is an identifier string — never number-coerce it. A
   // leading-zero code like '007' must persist verbatim (not collapse to 7).
   if (kp === 'project_code') {

src/core-utils.cts

@@ -178,7 +178,10 @@ function timeAgo(date: Date): string {
 function extractCanonicalPlanId(filename: string): string {
   const base = filename.replace(/-PLAN\.md$/i, '').replace(/-SUMMARY\.md$/i, '').replace(/\.md$/i, '');
   const parts = base.split('-').filter(Boolean);
-  const tokenRe = /^\d+[A-Z]?(?:\.\d+)*$/i;
+  // #2043: a phase/plan token component is either a zero-padded number (≥2 digits)
+  // or a single-digit-plus-letter id ("3A"); a *bare* single digit is a slug word,
+  // so "46-6-rs-…" is not paired into a "46-6" id while "3A-01" stays intact.
+  const tokenRe = /^(?:\d{2,}[A-Z]?|\d[A-Z])(?:\.\d+)*$/i;
   const phaseIdx = parts.findIndex(p => tokenRe.test(p));
   if (phaseIdx >= 0 && phaseIdx + 1 < parts.length && tokenRe.test(parts[phaseIdx + 1])) {
     return `${parts[phaseIdx]}-${parts[phaseIdx + 1]}`;

src/phase-id.cts

@@ -205,9 +205,29 @@ function extractPhaseToken(dirName: string): string {
 
   const segments = rest.split('-');
   const tokenSegments: string[] = [];
+  // #2043: distinguish a real (zero-padded, ≥2-digit) phase/sub-phase segment
+  // from a single-digit slug word. A pure-numeric leading segment ("46") only
+  // continues with ≥2-digit segments, so "46-6-rs-…" yields "46" (the "6" is the
+  // slug's first word), not "46-6". Milestone-prefixed ids like "M1-2" reach here
+  // with "M1-" already stripped as a project-code prefix (see
+  // PROJECT_CODE_PREFIX_CAPTURE_RE_I), so "2" is the leading segment and the same
+  // pure-numeric rule applies (M1-46-6-rs → "M1-46"). The firstLetterPrefixed
+  // carve-out covers letter+digit leading segments that survive prefix stripping
+  // because of punctuation (e.g. "P0.3-2"), whose single-digit continuation is
+  // intentionally preserved (unchanged from prior behaviour).
+  let firstLetterPrefixed = false;
   for (let i = 0; i < segments.length; i++) {
     const seg = segments[i];
-    if (/^\d/.test(seg) || (i === 0 && /^[A-Za-z]{1,3}\d/.test(seg))) {
+    if (i === 0) {
+      if (/^\d/.test(seg)) {
+        tokenSegments.push(seg);
+      } else if (/^[A-Za-z]{1,3}\d/.test(seg)) {
+        tokenSegments.push(seg);
+        firstLetterPrefixed = true;
+      } else {
+        break;
+      }
+    } else if (/^\d{2,}/.test(seg) || (firstLetterPrefixed && /^\d/.test(seg))) {
       tokenSegments.push(seg);
     } else {
       break;

src/phase.cts

@@ -104,7 +104,10 @@ function extractCanonicalPlanId(filename: string): string {
     .replace(/-SUMMARY\.md$/i, '')
     .replace(/\.md$/i, '');
   const parts = base.split('-').filter(Boolean);
-  const tokenRe = /^\d+[A-Z]?(?:\.\d+)*$/i;
+  // #2043: a phase/plan token component is either a zero-padded number (≥2 digits)
+  // or a single-digit-plus-letter id ("3A"); a *bare* single digit is a slug word,
+  // so "46-6-rs-…" is not paired into a "46-6" id while "3A-01" stays intact.
+  const tokenRe = /^(?:\d{2,}[A-Z]?|\d[A-Z])(?:\.\d+)*$/i;
   const phaseIdx = parts.findIndex((p) => tokenRe.test(p));
   if (phaseIdx >= 0 && phaseIdx + 1 < parts.length && tokenRe.test(parts[phaseIdx + 1])) {
     return `${parts[phaseIdx]}-${parts[phaseIdx + 1]}`;

src/roadmap-parser.cts

@@ -469,8 +469,12 @@ function getMilestonePhaseFilter(cwd: string, versionOverride?: string | null, p
   }
 
   const roadmapUsesHyphenedIds = [...normalized].some(n => n.includes('-'));
+  // #2043: milestone-prefixed sub-phase components must be zero-padded (≥2 digits)
+  // — "-\d{2,}" instead of "-0*\d+" — so a single-digit slug word after the phase
+  // number (e.g. dir "46-6-rs-…") captures "46" and is not silently excluded from
+  // the milestone as a bogus "46-6" id.
   const numericRe = roadmapUsesHyphenedIds
-    ? /^0*(\d+(?:-0*\d+)*[A-Za-z]?(?:\.\d+)*)/
+    ? /^0*(\d+(?:-\d{2,})*[A-Za-z]?(?:\.\d+)*)/
     : /^0*(\d+[A-Za-z]?(?:\.\d+)*)/;
 
   function isDirInMilestone(dirName: string): boolean {

src/validate.cts

@@ -44,16 +44,25 @@ export const phaseDirNameRe = new RegExp(
 );
 // Extracts the full phase token from a directory name, including milestone-prefixed
 // multi-segment tokens like "02-01" from "02-01-setup" or "GSD-02-01-setup".
-// Greedily captures all leading all-digit segments before the first letter-start segment.
+// #2043: a *continuation* sub-phase segment must be zero-padded (≥2 digits), so a
+// single-digit slug word after a phase number (e.g. "46-6-rs-…", slug "6 Rs …") is
+// NOT absorbed — it captures "46", not "46-6". The first component stays "\d+"
+// (with the "[A-Z]?" suffix) so single-digit letter-suffixed phase ids ("1A") and
+// milestone-prefixed single-digit sub-phases ("M1-2" → prefix "M1-" stripped, then
+// "2") still match. The trailing boundary "(?:-|$)" (was "(?:-[a-z]|$)") lets a slug
+// that starts with a digit terminate the token.
 export const PHASE_TOKEN_FROM_DIR_RE = new RegExp(
-  `^${OPTIONAL_PROJECT_CODE_PREFIX_SOURCE}(\\d+(?:-\\d+)*[A-Z]?(?:\\.\\d+)*)(?:-[a-z]|$)`,
+  `^${OPTIONAL_PROJECT_CODE_PREFIX_SOURCE}(\\d+(?:-\\d{2,})*[A-Z]?(?:\\.\\d+)*)(?:-|$)`,
   'i',
 );
 export const MILESTONE_ARCHIVE_DIR_RE = /^v\d+.*-phases$/i;
 
 // ── Issue #26: I001 canonicalization ────────────────────────────────────────
 export function canonicalPlanStem(stem: string): string {
-  const m = stem.match(/^(\d+[A-Z]?(?:\.\d+)*-\d+)/i);
+  // #2043: the plan component (after the phase number) must be zero-padded
+  // (≥2 digits), so a digit-leading slug word (e.g. "46-6-rs-…") is not mistaken
+  // for a "46-6" phase/plan pair.
+  const m = stem.match(/^(\d+[A-Z]?(?:\.\d+)*-\d{2,})/i);
   return m ? m[1] : stem;
 }
 

tests/config.test.cjs

@@ -747,6 +747,131 @@ describe('config-set — no silent coercion (#1581)', () => {
   });
 });
 
+// ─── config-set <key> null — unset/clear (#2046) ─────────────────────────────
+
+describe('config-set <key> null — unset/clear (#2046)', () => {
+  let tmpDir;
+
+  beforeEach(() => { tmpDir = createTempProject(); });
+  afterEach(() => { cleanup(tmpDir); });
+
+  test('non-secret routing key: config-set <key> null removes the key (not the string "null")', () => {
+    const setResult = runGsdTools('config-set review.models.gemini foo', tmpDir);
+    assert.ok(setResult.success, `Command failed: ${setResult.error}`);
+    assert.strictEqual(readConfig(tmpDir).review.models.gemini, 'foo');
+
+    const unsetResult = runGsdTools('config-set review.models.gemini null', tmpDir);
+    assert.ok(unsetResult.success, `Command failed: ${unsetResult.error}`);
+
+    const config = readConfig(tmpDir);
+    assert.ok(
+      !config.review || !config.review.models || !Object.prototype.hasOwnProperty.call(config.review.models, 'gemini'),
+      'review.models.gemini must be absent on disk after unset, not the string "null"'
+    );
+
+    const getResult = runGsdTools('config-get review.models.gemini', tmpDir);
+    assert.ok(
+      !getResult.output || !getResult.output.trim() || getResult.output.trim() === 'undefined',
+      `config-get should return empty/undefined after unset, got: ${getResult.output}`
+    );
+    assert.notStrictEqual(getResult.output && getResult.output.trim(), 'null');
+  });
+
+  test('secret key: config-set brave_search null removes the key (never persists "null")', () => {
+    const setResult = runGsdTools('config-set brave_search sk-test-1234', tmpDir);
+    assert.ok(setResult.success, `Command failed: ${setResult.error}`);
+    assert.strictEqual(readConfig(tmpDir).brave_search, 'sk-test-1234');
+
+    const unsetResult = runGsdTools('config-set brave_search null', tmpDir);
+    assert.ok(unsetResult.success, `Command failed: ${unsetResult.error}`);
+
+    const configPath = path.join(tmpDir, '.planning', 'config.json');
+    const rawText = fs.readFileSync(configPath, 'utf-8');
+    const config = JSON.parse(rawText);
+    assert.ok(
+      !Object.prototype.hasOwnProperty.call(config, 'brave_search'),
+      'brave_search must be absent on disk after unset'
+    );
+    assert.doesNotMatch(rawText, /"brave_search":\s*"null"/,
+      'raw config.json must never contain brave_search mapped to the literal string "null"');
+  });
+
+  test('typed-key bypass: config-set context null clears an enum-typed key without validator rejection', () => {
+    const setResult = runGsdTools('config-set context dev', tmpDir);
+    assert.ok(setResult.success, `Command failed: ${setResult.error}`);
+    assert.strictEqual(readConfig(tmpDir).context, 'dev');
+
+    const unsetResult = runGsdTools('config-set context null', tmpDir);
+    assert.ok(unsetResult.success, `config-set context null must succeed (bypass enum validator), got error: ${unsetResult.error}`);
+
+    const config = readConfig(tmpDir);
+    assert.ok(!Object.prototype.hasOwnProperty.call(config, 'context'),
+      'context key must be removed after unset');
+  });
+
+  test('idempotent: config-set <never-set key> null succeeds with no crash and no key written', () => {
+    const result = runGsdTools('config-set git.base_branch null', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const config = readConfig(tmpDir);
+    assert.ok(
+      !config.git || !Object.prototype.hasOwnProperty.call(config.git, 'base_branch'),
+      'git.base_branch must not be present after unsetting a key that was never set'
+    );
+  });
+
+  test('literal-"null" guard: no config-set <key> null ever persists the literal string "null" on disk', () => {
+    runGsdTools('config-set review.models.gemini foo', tmpDir);
+    runGsdTools('config-set review.models.gemini null', tmpDir);
+    runGsdTools('config-set brave_search sk-test-1234', tmpDir);
+    runGsdTools('config-set brave_search null', tmpDir);
+    runGsdTools('config-set context dev', tmpDir);
+    runGsdTools('config-set context null', tmpDir);
+
+    const configPath = path.join(tmpDir, '.planning', 'config.json');
+    const rawText = fs.readFileSync(configPath, 'utf-8');
+    assert.doesNotMatch(rawText, /:\s*"null"/,
+      `config.json must never contain a key mapped to the literal string "null": ${rawText}`);
+  });
+
+  test('prototype-pollution guard: unsetting a __proto__ leaf is rejected, no pollution (alert #26 parity)', () => {
+    // Create the intermediate so the unset walk reaches the leaf guard (a bare
+    // dynamic-prefix key passes the schema gate, so this exercises the
+    // _unsetNestedValue guard, not the schema gate — mirrors the set-path test).
+    const seed = runGsdTools('config-set agent_skills.sonnet-coder true', tmpDir);
+    assert.ok(seed.success, `seed failed: ${seed.error}`);
+
+    const result = runGsdTools('config-set agent_skills.__proto__ null', tmpDir);
+    assert.strictEqual(result.success, false, `Expected rejection, got: ${result.output}`);
+    assert.ok(
+      result.error.includes('prototype pollution guard'),
+      `Expected pollution-guard error, got: ${result.error}`,
+    );
+    // No prototype pollution occurred via the unset path.
+    assert.strictEqual(({}).polluted, undefined);
+    assert.strictEqual(Object.prototype.hasOwnProperty.call(Object.prototype, 'polluted'), false);
+  });
+
+  test('deep (4-segment) nested key: config-set <deep> null removes only the leaf', () => {
+    const set = runGsdTools('config-set review.reviewer_instances.myinst.model some-model', tmpDir);
+    assert.ok(set.success, `deep set failed: ${set.error}`);
+    assert.strictEqual(readConfig(tmpDir).review.reviewer_instances.myinst.model, 'some-model');
+
+    const unset = runGsdTools('config-set review.reviewer_instances.myinst.model null', tmpDir);
+    assert.ok(unset.success, `deep unset failed: ${unset.error}`);
+
+    const config = readConfig(tmpDir);
+    assert.ok(
+      !config.review.reviewer_instances.myinst ||
+        !Object.prototype.hasOwnProperty.call(config.review.reviewer_instances.myinst, 'model'),
+      'the leaf model key must be removed',
+    );
+    // Parent objects along the path are preserved (unset removes only the leaf).
+    assert.ok(config.review && config.review.reviewer_instances,
+      'parent objects on the path must remain after leaf unset');
+  });
+});
+
 // ─── config-set (research_before_questions and discuss_mode) ──────────────────
 
 describe('config-set research_before_questions and discuss_mode', () => {

tests/core-utils.test.cjs

@@ -533,6 +533,21 @@ describe('extractCanonicalPlanId', () => {
     assert.ok(typeof result === 'string');
     assert.ok(result.length > 0);
   });
+
+  test('rejects single-digit slug word (#2043)', () => {
+    // "46-6-rs-pipeline-orchestrator" is not a valid phase-token filename shape
+    // (the "6" is a slug word, not a sub-phase segment) — must not collapse to
+    // the pre-fix, buggy "46-6".
+    assert.notStrictEqual(
+      coreUtils.extractCanonicalPlanId('46-6-rs-pipeline-orchestrator'),
+      '46-6',
+    );
+    // Legit multi-segment phase-token filenames are still extracted correctly,
+    // including a single-digit letter-suffix phase id ("3A") — the "3A" token is
+    // found and paired with its zero-padded plan index, not left unpaired.
+    assert.strictEqual(coreUtils.extractCanonicalPlanId('01-02-PLAN.md'), '01-02');
+    assert.strictEqual(coreUtils.extractCanonicalPlanId('3A-01-feature-PLAN.md'), '3A-01');
+  });
 });
 
 // ─── countMatchedSummaries (#1988) ───────────────────────────────────────────

tests/health-validation.test.cjs

@@ -1132,6 +1132,23 @@ describe('Drift item W006-archived — MILESTONE_ARCHIVE_DIR_RE and PHASE_TOKEN_
     assert.strictEqual(re.exec('APP1-64-auth')?.[1], '64');
     assert.strictEqual(re.exec('APP_1-64-auth')?.[1], '64');
   });
+
+  test('PHASE_TOKEN_FROM_DIR_RE rejects a single-digit slug word after a phase number (#2043)', () => {
+    const gen = require('../gsd-core/bin/lib/validate.cjs');
+    const re = gen.PHASE_TOKEN_FROM_DIR_RE;
+    // Roadmap phase name "6 Rs Pipeline Orchestrator" slugifies to
+    // "6-rs-pipeline-orchestrator"; the resulting dir "46-6-rs-pipeline-orchestrator"
+    // must extract phase token "46", not "46-6" (was the pre-fix, buggy behavior).
+    assert.strictEqual(re.exec('46-6-rs-pipeline-orchestrator')?.[1], '46');
+    // Legit multi-segment (zero-padded) milestone-prefixed tokens are preserved.
+    assert.strictEqual(re.exec('02-01-setup')?.[1], '02-01');
+    // Single-digit letter-suffix phase ids ("1A"/"01A") and milestone-prefixed
+    // single-digit sub-phases ("M1-2" → "2") must still match (the fix tightens
+    // only the continuation, not the first component).
+    assert.strictEqual(re.exec('1A-foo')?.[1], '1A');
+    assert.strictEqual(re.exec('01A-foo')?.[1], '01A');
+    assert.strictEqual(re.exec('M1-2-setup')?.[1], '2');
+  });
 });
 
 // ── Drift Item I001: canonicalPlanStem ────────────────────────────────────────
@@ -1186,6 +1203,18 @@ describe('Drift item I001 — canonicalPlanStem: long PLAN stem matches short SU
     assert.strictEqual(gen.canonicalPlanStem('3A-01-feature'), '3A-01');
     assert.strictEqual(gen.canonicalPlanStem('no-match'), 'no-match');
   });
+
+  test('canonicalPlanStem rejects a single-digit slug word after a phase number (#2043)', () => {
+    const gen = require('../gsd-core/bin/lib/validate.cjs');
+    // "46-6-rs-pipeline-orchestrator" is not a valid PLAN stem shape (the "6"
+    // is a slug word, not a sub-phase segment), so it must return the input
+    // unchanged rather than the pre-fix, buggy "46-6".
+    assert.notStrictEqual(gen.canonicalPlanStem('46-6-rs-pipeline-orchestrator'), '46-6');
+    // Legit multi-segment stems are still canonicalized correctly, including a
+    // single-digit letter-suffix phase id ("3A") whose plan component is zero-padded.
+    assert.strictEqual(gen.canonicalPlanStem('68-01-scaffolding'), '68-01');
+    assert.strictEqual(gen.canonicalPlanStem('3A-01-feature'), '3A-01');
+  });
 });
   });
 }

tests/phase-id.test.cjs

@@ -217,6 +217,27 @@ describe('extractPhaseToken', () => {
   test('stops at first non-numeric-starting segment', () => {
     assert.strictEqual(phaseId.extractPhaseToken('01-02-name-03'), '01-02');
   });
+
+  test('rejects a single-digit slug word after a phase number (#2043)', () => {
+    // A phase dir like "46-6-rs-pipeline-orchestrator" (roadmap phase name
+    // "6 Rs Pipeline Orchestrator" → slug "6-rs-...") must yield token "46",
+    // not "46-6" — the "6" is the slug's first word, not a sub-phase segment.
+    assert.strictEqual(phaseId.extractPhaseToken('46-6-rs-pipeline-orchestrator'), '46');
+    assert.strictEqual(phaseId.extractPhaseToken('68-6-rs'), '68');
+    // Legit cases are unaffected: a real zero-padded milestone-sub-phase pair
+    // stays intact, and a single-digit sub-phase after a letter-prefixed
+    // milestone id (e.g. "M1-2") is still valid.
+    assert.strictEqual(phaseId.extractPhaseToken('01-02-some-name'), '01-02');
+    assert.strictEqual(phaseId.extractPhaseToken('M1-2-brain'), 'M1-2');
+    // Milestone-prefixed convention: "M1-" strips as a project-code prefix, so
+    // the same rule fixes the slug-collision there too — a phase 46 named
+    // "6 Rs …" under milestone M1 yields "M1-46", not "M1-46-6". Phase 6 under
+    // M1 ("M1-6-rs") correctly stays "M1-6" (the 6 is the phase number).
+    assert.strictEqual(phaseId.extractPhaseToken('M1-46-6-rs-pipeline-orchestrator'), 'M1-46');
+    assert.strictEqual(phaseId.extractPhaseToken('M1-6-rs-pipeline'), 'M1-6');
+    // Single-digit + letter-suffix phase id ("1A") is a real token, not a slug word.
+    assert.strictEqual(phaseId.extractPhaseToken('1A-brain'), '1A');
+  });
 });
 
 // ─── phaseTokenMatches ────────────────────────────────────────────────────────

tests/review-model-config.test.cjs

@@ -4,11 +4,14 @@
  * Verifies the review.models.<cli> dynamic config key pattern:
  *   - isValidConfigKey accepts review.models.<cli-name>
  *   - validateKnownConfigKeyPath suggests review.models.<cli-name> for review.model
- *   - End-to-end round-trip via config-set / config-get for both model IDs and null
+ *   - End-to-end round-trip via config-set / config-get for model IDs and the
+ *     null "Clear" action (#2046 — config-set <key> null unsets the key)
  */
 
 const { test, describe, beforeEach, afterEach } = require('node:test');
 const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
 const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 
 describe('review.models.<cli> config key', () => {
@@ -110,28 +113,49 @@ describe('review.models.<cli> config key', () => {
     );
   });
 
-  test('round-trip: config-set null then config-get returns "null"', () => {
-    // The issue spec documents null as the "fall back to CLI default" sentinel.
-    // cmdConfigSet does not parse 'null' as JSON null — it stores the literal
-    // string 'null'. config-get --raw returns the string 'null', and the
-    // workflow's `[ "$VAR" != "null" ]` guard handles this.
+  test('round-trip: config-set null UNSETS the model key (#2046 — the "Clear" action)', () => {
+    // #2046: `config-set <key> null` now DELETES the key (the documented "Clear"
+    // action) instead of persisting the literal string "null". A previously-set
+    // model override is removed cleanly; config-get then reports key-not-found.
+    // The review workflow's guard (`[ -n "$VAR" ] && [ "$VAR" != "null" ]`,
+    // review.md:259) treats the resulting empty read as "no override → use the
+    // reviewer's default", exactly as it treated the old "null" sentinel.
     const setResult = runGsdTools(
+      ['config-set', 'review.models.gemini', 'gemini-3.1-pro-preview'],
+      tmpDir,
+      { HOME: tmpDir, USERPROFILE: tmpDir }
+    );
+    assert.ok(setResult.success, `config-set failed: ${setResult.error}`);
+
+    const clearResult = runGsdTools(
       ['config-set', 'review.models.gemini', 'null'],
       tmpDir,
       { HOME: tmpDir, USERPROFILE: tmpDir }
     );
-    assert.ok(setResult.success, `config-set null failed: ${setResult.error}`);
+    assert.ok(clearResult.success, `config-set null failed: ${clearResult.error}`);
 
+    // The key is gone from disk — not persisted as the string "null".
+    const configPath = path.join(tmpDir, '.planning', 'config.json');
+    const rawText = fs.readFileSync(configPath, 'utf-8');
+    const config = JSON.parse(rawText);
+    assert.ok(
+      !config.review || !config.review.models ||
+        !Object.prototype.hasOwnProperty.call(config.review.models, 'gemini'),
+      `review.models.gemini must be absent after clear, got: ${rawText}`
+    );
+    assert.doesNotMatch(rawText, /"gemini":\s*"null"/,
+      'must never persist review.models.gemini as the literal string "null"');
+
+    // config-get on the removed key reports not-found (the review workflow reads
+    // it as `... 2>/dev/null || echo ""` → empty → the `[ -n "$VAR" ]` guard falls
+    // back to the reviewer default).
     const getResult = runGsdTools(
       ['config-get', 'review.models.gemini', '--raw'],
       tmpDir,
       { HOME: tmpDir, USERPROFILE: tmpDir }
     );
-    assert.ok(getResult.success, `config-get failed: ${getResult.error}`);
-    assert.strictEqual(
-      getResult.output,
-      'null',
-      'config-get should return the literal string "null" so the workflow guard can match it'
-    );
+    assert.ok(!getResult.success, 'config-get on a cleared key should report not-found');
+    assert.notStrictEqual(getResult.output && getResult.output.trim(), 'null',
+      'config-get must not emit the literal string "null" for a cleared key');
   });
 });

tests/roadmap-parser.test.cjs

@@ -428,6 +428,34 @@ describe('roadmap-parser: getMilestonePhaseFilter', () => {
     assert.strictEqual(filter('02-03-other'), false, '02-03 not in milestone');
   });
 
+  test('single-digit slug word after a phase number is not wrongly excluded (#2043)', () => {
+    // The roadmap uses milestone-prefixed hyphenated phase IDs (e.g. "2-01"),
+    // which switches getMilestonePhaseFilter's dir-matching regex into
+    // hyphenated mode. Phase 46's roadmap name "6 Rs Pipeline Orchestrator"
+    // slugifies to a dir starting with a single-digit word ("46-6-rs-…").
+    // Before #2043, the hyphenated-mode regex over-collected that single
+    // digit into the phase token ("46-6"), which never matched the roadmap's
+    // "46" phase number, so the dir was wrongly excluded from the milestone.
+    writeState(tmpDir, { milestone: 'v1.0' });
+    writeRoadmap(tmpDir, [
+      '## v1.0: Current',
+      '### Phase 2-01: Alpha',
+      '**Goal:** first alpha phase',
+      '',
+      '### Phase 46: 6 Rs Pipeline Orchestrator',
+      '**Goal:** orchestrate the rs',
+    ].join('\n'));
+
+    const filter = getMilestonePhaseFilter(tmpDir);
+    assert.strictEqual(
+      filter('46-6-rs-pipeline-orchestrator'),
+      true,
+      '46-6-rs-pipeline-orchestrator (phase 46, single-digit slug word "6") must match Phase 46',
+    );
+    // Legit milestone-prefixed dir still matches as before.
+    assert.strictEqual(filter('02-01-alpha'), true, '02-01-alpha matches Phase 2-01');
+  });
+
   test('versionOverride uses specified version slice', () => {
     writeRoadmap(tmpDir, [
       '## v1.0: Old',