@zigrivers/scaffold 3.14.0 → 3.16.0

package/content/tools/review-pr.md

@@ -1,6 +1,6 @@
 ---
 name: review-pr
-description: Run all configured code review channels on a PR (Codex CLI, Gemini CLI, Superpowers code-reviewer)
+description: Run all configured code review channels on a PR (Codex CLI, Gemini CLI, Claude CLI)
 phase: null
 order: null
 dependencies: []
@@ -21,15 +21,16 @@ of remembering three separate review invocations.
 The three channels are:
 1. **Codex CLI** — OpenAI's code analysis (implementation correctness, security, API contracts)
 2. **Gemini CLI** — Google's design reasoning (architectural patterns, broad context)
-3. **Superpowers code-reviewer** — Claude subagent review (plan alignment, code quality, testing)
+3. **Claude CLI** — Anthropic's code review (plan alignment, code quality, testing)
 
 ## Inputs
 
 - $ARGUMENTS — PR number (optional; auto-detected from current branch if omitted)
-- docs/review-standards.md (optional) — severity definitions and review criteria
-- docs/coding-standards.md (required) — coding conventions for review context
-- docs/tdd-standards.md (optional) — test coverage expectations
-- AGENTS.md (optional) — reviewer instructions with project-specific rules
+- `.mmr.yaml` — MMR CLI configuration (channels, review_criteria, defaults)
+
+The CLI handles review context via config (`review_criteria` in `.mmr.yaml`).
+Project-specific standards (coding-standards, review-standards) are referenced
+in the review criteria config rather than read at dispatch time.
 
 ## Expected Outputs
 
@@ -48,119 +49,98 @@ PR_NUMBER="${ARGUMENTS:-$(gh pr view --json number -q .number 2>/dev/null)}"
 
 If no PR is found, stop and tell the user to create a PR first.
 
-### Step 2: Gather Review Context
+### Step 2: Run MMR Review
 
-Collect the PR diff and project standards for review prompts:
+Use the MMR CLI as the primary entry point for automated dispatch, reconciliation, and verdict:
 
 ```bash
-PR_DIFF=$(gh pr diff "$PR_NUMBER")
+MMR_RESULT=$(mmr review --pr "$PR_NUMBER" --sync --format json)
+# Extract job_id from JSON output for use in mmr reconcile
+JOB_ID=$(echo "$MMR_RESULT" | grep -o '"job_id": "[^"]*"' | head -1 | cut -d'"' -f4)
 ```
 
-Read these files for review context (skip any that don't exist):
-- `docs/coding-standards.md`
-- `docs/tdd-standards.md`
-- `docs/review-standards.md`
-- `AGENTS.md`
+The CLI handles:
+- Installation and auth checks for each channel (codex, gemini, claude)
+- Compensating passes when channels are unavailable (dispatched via `claude -p`)
+- Output parsing and finding reconciliation
+- Verdict derivation (pass/degraded-pass/blocked/needs-user-decision)
+- Exit codes: 0=pass/degraded-pass, 2=blocked, 3=needs-user-decision
 
-### Step 3: Run All Three Review Channels
+The CLI supports multiple input modes:
+- `--pr <number>` — review a GitHub PR (fetches diff via `gh pr diff`)
+- `--diff <file>` — review a diff file
+- `--staged` — review staged changes (`git diff --cached`)
+- `--base <ref> --head <ref>` — review diff between two refs
 
-Run all three channels. Track which ones complete successfully.
+**Manual fallback** (when MMR CLI is not installed):
 
-**Foreground only:** Always run Codex and Gemini CLI commands as foreground Bash calls. Never use `run_in_background`, `&`, or `nohup`. Background execution produces empty output.
+Run Codex, Gemini, and Claude CLI commands individually as foreground Bash calls.
+Never use `run_in_background`, `&`, or `nohup`.
 
 #### Channel 1: Codex CLI
 
-**Installation check:**
-```bash
-command -v codex >/dev/null 2>&1
-```
-- If `codex` is not installed: queue a compensating Claude self-review pass focused on implementation correctness, security, and API contracts. Record root-cause `not_installed`. Skip to next channel.
-
-**Auth check first** (auth tokens expire — always re-verify):
-
-```bash
-codex login status 2>/dev/null && echo "codex authenticated" || echo "codex NOT authenticated"
-```
-
-If auth fails, tell the user: "Codex auth expired. Run: `! codex login`" — do NOT
-silently fall back. After the user re-authenticates, retry.
-
-If auth cannot be recovered, queue a compensating pass (same focus as above). Record root-cause `auth_failed`.
-If auth check times out (~5s), retry once. If still failing, record root-cause `auth_timeout` and queue compensating pass.
-
-**Run the review:**
-
 ```bash
+command -v codex >/dev/null 2>&1 || echo "Codex not installed"
+codex login status 2>/dev/null
 codex exec --skip-git-repo-check -s read-only --ephemeral "REVIEW_PROMPT" 2>/dev/null
 ```
 
-The review prompt must include:
-- The PR diff
-- Coding standards from docs/coding-standards.md
-- Review standards from docs/review-standards.md (if exists)
-- Instruction to report P0/P1/P2 findings as JSON with severity, location (file:line), description, and suggestion
-
-If the CLI exits with a non-zero code, produces malformed/unparseable output, or is killed by the tool runner timeout, record root-cause `failed` and queue a compensating pass for that channel.
+If not installed or auth fails, queue a compensating pass focused on implementation
+correctness, security, and API contracts. Auth failure recovery: `! codex login`.
 
 #### Channel 2: Gemini CLI
 
-**Installation check:**
 ```bash
-command -v gemini >/dev/null 2>&1
+command -v gemini >/dev/null 2>&1 || echo "Gemini not installed"
+NO_BROWSER=true gemini -p "respond with ok" -o json 2>&1
+NO_BROWSER=true gemini -p "REVIEW_PROMPT" --output-format json --approval-mode yolo 2>/dev/null
 ```
-- If `gemini` is not installed: queue a compensating Claude self-review pass focused on architectural patterns, design reasoning, and broad context. Record root-cause `not_installed`. Label findings as `[compensating: Gemini-equivalent]`. Skip to next channel.
 
-**Auth check first:**
+If not installed or auth fails, queue a compensating pass focused on architectural
+patterns, design reasoning, and broad context. Auth failure recovery: `! gemini -p "hello"`.
+
+#### Channel 3: Claude CLI
 
 ```bash
-GEMINI_AUTH_CHECK=$(NO_BROWSER=true gemini -p "respond with ok" -o json 2>&1)
-GEMINI_EXIT=$?
-if [ "$GEMINI_EXIT" -eq 0 ]; then
-  echo "gemini authenticated"
-elif [ "$GEMINI_EXIT" -eq 41 ]; then
-  echo "gemini NOT authenticated (exit 41: auth error)"
-fi
+claude -p "REVIEW_PROMPT" --output-format json 2>/dev/null
 ```
 
-If auth fails (exit 41), tell the user: "Gemini auth expired. Run: `! gemini -p \"hello\"`" — do NOT silently fall back. After the user re-authenticates, retry.
+Claude CLI handles its own auth. Focus: plan alignment, code quality, testing.
 
-If auth cannot be recovered, queue a compensating pass focused on architectural patterns, design reasoning, and broad context. Record root-cause `auth_failed`. Label findings as `[compensating: Gemini-equivalent]`.
-If auth check times out (~5s), retry once. If still failing, record root-cause `auth_timeout` and queue compensating pass labeled `[compensating: Gemini-equivalent]`.
+**After all channels:** Run any queued compensating passes as additional `claude -p`
+dispatches with focused prompts. Label findings as `[compensating: Codex-equivalent]`
+or `[compensating: Gemini-equivalent]`.
 
-**Run the review:**
+### Step 3: Run Agent Code Review (4th channel)
 
-```bash
-NO_BROWSER=true gemini -p "REVIEW_PROMPT" --output-format json --approval-mode yolo 2>/dev/null
-```
+Dispatch your platform's code-reviewer skill for a complementary review:
+- **Claude Code:** dispatch `superpowers:code-reviewer` subagent with the PR diff and review criteria
+- **Other platforms:** use your platform's equivalent agent review skill
 
-Same review prompt content as Codex. Do NOT share one model's output with the other —
-each reviews independently.
+The agent skill runs inside your agent's context — it has access to conversation history, project knowledge, and plan context that external CLIs lack.
 
-If the CLI exits with a non-zero code, produces malformed/unparseable output, or is killed by the tool runner timeout, record root-cause `failed` and queue a compensating pass for that channel.
+**Important:** The agent's review output must use MMR-compatible finding schema: each finding needs `severity` (P0-P3), `location` (file:line), and `description` (`suggestion` is optional). The strict validator in `mmr reconcile` will reject findings with missing or invalid required fields.
 
-#### Channel 3: Superpowers Code-Reviewer Subagent
+### Step 4: Inject Agent Review into MMR
 
-Dispatch the `superpowers:code-reviewer` subagent. This channel always runs (it uses
-Claude, which is always available).
+Feed the agent review findings into MMR for unified reconciliation:
 
 ```bash
-BASE_SHA=$(gh pr view "$PR_NUMBER" --json baseRefOid -q .baseRefOid)
-HEAD_SHA=$(gh pr view "$PR_NUMBER" --json headRefOid -q .headRefOid)
+# job_id is captured from mmr review --sync --format json output
+# Write agent findings to a temp file for mmr reconcile
+echo "$AGENT_FINDINGS" > /tmp/agent-findings.json
+mmr reconcile "$JOB_ID" --channel superpowers --input /tmp/agent-findings.json
 ```
 
-Dispatch with the Agent tool using `superpowers:code-reviewer` as the subagent type,
-providing:
-- `WHAT_WAS_IMPLEMENTED` — PR title and description
-- `PLAN_OR_REQUIREMENTS` — coding standards and review standards
-- `BASE_SHA` — base commit
-- `HEAD_SHA` — head commit
-- `DESCRIPTION` — PR summary
+The `reconcile` command:
+- Adds the agent's findings as a new channel in the job
+- Re-runs reconciliation across ALL channels (CLI + agent)
+- Outputs the unified verdict with all sources included
 
-**After all channels:** Run any queued compensating passes as foreground Claude self-review passes. Each uses the same review prompt as the missing channel, focused on that channel's strength area. Label findings as `[compensating: Codex-equivalent]` or `[compensating: Gemini-equivalent]`.
+### Step 5: Reconcile Findings
 
-### Step 4: Reconcile Findings
-
-After all channels complete, reconcile findings:
+When using `mmr review --sync`, reconciliation is automatic. For manual fallback,
+reconcile findings after all channels complete:
 
 | Scenario | Confidence | Action |
 |----------|-----------|--------|
@@ -171,7 +151,7 @@ After all channels complete, reconcile findings:
 | Channels contradict each other | **Low** | Present to user for adjudication |
 | Compensating-pass P0/P1/P2 finding | **Single-source** | Fix per normal thresholds, label as compensating |
 
-### Step 5: Report Results
+### Step 6: Report Results
 
 Output a review summary in this format:
 
@@ -179,9 +159,10 @@ Output a review summary in this format:
 ## Code Review Summary — PR #[number]
 
 ### Channels Executed
-- [ ] Codex CLI — root cause: [completed / not installed / auth failed / auth timeout / failed], coverage: [full / compensating (Codex-equivalent)]
-- [ ] Gemini CLI — root cause: [completed / not installed / auth failed / auth timeout / failed], coverage: [full / compensating (Gemini-equivalent)]
-- [ ] Superpowers code-reviewer — [completed / failed]
+- [ ] Codex CLI — root cause: [completed / not installed / auth failed / timeout / failed], coverage: [full / compensating (Codex-equivalent)]
+- [ ] Gemini CLI — root cause: [completed / not installed / auth failed / timeout / failed], coverage: [full / compensating (Gemini-equivalent)]
+- [ ] Claude CLI — root cause: [completed / not_installed / auth_failed / timeout / failed], coverage: [full / compensating]
+- [ ] Agent review — [completed / skipped], injected via mmr reconcile
 
 ### Consensus Findings (High Confidence)
 [Findings flagged by 2+ channels]
@@ -196,7 +177,7 @@ Output a review summary in this format:
 [pass / degraded-pass / blocked / needs-user-decision]
 ```
 
-### Step 5a: Final Verdict
+### Step 6a: Final Verdict
 
 Return exactly one verdict:
 
@@ -209,17 +190,19 @@ Verdict precedence: `needs-user-decision` > `blocked` > `degraded-pass` > `pass`
 
 When compensating passes ran, maximum achievable verdict is `degraded-pass`. When both external channels were compensated, note "All findings are single-model."
 
-### Step 6: Fix P0/P1/P2 Findings
+### Step 7: Fix P0/P1/P2 Findings
 
 If any P0, P1, or P2 findings exist:
 1. Fix them in the code
 2. Push the fixes: `git push`
-3. Re-run the channels that produced findings to verify fixes
+3. Re-run the review to verify fixes: `mmr review --pr "$PR_NUMBER" --sync --format json`
 4. After 3 fix rounds with unresolved P0/P1/P2 findings, stop and ask the user for direction — do NOT merge automatically. Document remaining findings and let the user decide whether to continue fixing, create follow-up issues, or override.
 
-**Fix cycle channel rule:** Re-run only channels that originally completed or ran as compensating passes. Never retry a channel marked `not installed`, `auth failed`, or `auth timeout` during fix rounds — its availability does not change within a session.
+**Note:** Fix cycles are an orchestration concern — the caller (agent or human) handles the fix loop. The CLI provides the review and verdict; the caller decides whether to fix and re-run.
+
+**Fix cycle channel rule:** Re-run only channels that originally completed or ran as compensating passes. Never retry a channel marked `not_installed`, `auth_failed`, or `timeout` during fix rounds — its availability does not change within a session.
 
-### Step 7: Confirm Completion
+### Step 8: Confirm Completion
 
 After all findings are resolved (or 3 rounds complete), output:
 
@@ -236,21 +219,22 @@ Do NOT proceed to the next task or merge until this confirmation is output.
 | Channel not installed | Queue compensating pass, report root-cause `not_installed` |
 | Auth expired, user recovers | Retry dispatch |
 | Auth expired, user declines | Queue compensating pass, report root-cause `auth_failed` |
-| Auth check timeout (after retry) | Queue compensating pass, report root-cause `auth_timeout` |
+| Auth check timeout (after retry) | Queue compensating pass, report root-cause `timeout` |
 | Channel fails during execution | Queue compensating pass, report root-cause `failed` |
 | Both external channels unavailable | Two compensating passes, max verdict: `degraded-pass`, note "All findings single-model" |
-| Superpowers unavailable | Run available CLIs, warn user (Superpowers is always-available Claude — no compensating pass) |
 
 ## Process Rules
 
-1. **Foreground only** — Always run Codex and Gemini CLI commands as foreground Bash calls. Never use `run_in_background`, `&`, or `nohup`.
-2. **All three channels are mandatory** — skip only when a tool is genuinely not installed, never by choice.
+1. **Foreground only** — Always run Codex, Gemini, and Claude CLI commands as foreground Bash calls. Never use `run_in_background`, `&`, or `nohup`.
+2. **All three channels are mandatory** — Codex CLI, Gemini CLI, and Claude CLI. Skip only when a tool is genuinely not installed, never by choice.
 3. **Auth failures are not silent** — always surface to the user with the exact recovery command.
 4. **Independence** — never share one channel's output with another. Each reviews the diff independently.
 5. **Fix before proceeding** — P0/P1/P2 findings must be resolved before moving to the next task.
 6. **3-round limit** — never attempt more than 3 fix rounds. Surface unresolved findings to the user.
 7. **Document everything** — the review summary must show which channels ran and which were skipped, with reasons.
-8. **Dispatch pattern** follows `multi-model-review-dispatch` knowledge entry. When modifying channel dispatch in this file, verify consistency with `review-code.md` and `post-implementation-review.md`.
+8. **CLI-first** — use `mmr review --sync` as the primary entry point. Manual dispatch is a fallback only.
+9. **Job storage** — the CLI stores job data at `~/.mmr/jobs/{job-id}/results.json`. Review results are available via `mmr results <job-id>`.
+10. **Dispatch pattern** follows `multi-model-review-dispatch` knowledge entry. When modifying channel dispatch in this file, verify consistency with `review-code.md` and `post-implementation-review.md`.
 
 ---
 

package/dist/cli/commands/adopt.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"adopt.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/adopt.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAQ,MAAM,OAAO,CAAA;AAYhD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAA;AAa5D,UAAU,SAAS;IACjB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,SAAS,EAAE,OAAO,CAAA;IAClB,cAAc,CAAC,EAAE,MAAM,CAAA;IAEvB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;CACvB;AAYD,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,cAAc,GACrB,IAAI,CAgDN;AAmDD,QAAA,MAAM,YAAY,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,CAgZnE,CAAA;AAED,eAAe,YAAY,CAAA"}
+{"version":3,"file":"adopt.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/adopt.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAQ,MAAM,OAAO,CAAA;AAYhD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAA;AAa5D,UAAU,SAAS;IACjB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,SAAS,EAAE,OAAO,CAAA;IAClB,cAAc,CAAC,EAAE,MAAM,CAAA;IAEvB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;CACvB;AAYD,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,cAAc,GACrB,IAAI,CAgDN;AAmDD,QAAA,MAAM,YAAY,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,CAqanE,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/cli/commands/adopt.js

@@ -11,7 +11,7 @@ import { getPackagePipelineDir } from '../../utils/fs.js';
 import { runAdoption, TYPE_KEY } from '../../project/adopt.js';
 import { ProjectTypeSchema } from '../../config/schema.js';
 import { coerceCSV } from '../utils/coerce.js';
-import { LIB_FLAGS, MOBILE_FLAGS, PIPELINE_FLAGS, ML_FLAGS, EXT_FLAGS, applyFlagFamilyValidation, buildFlagOverrides, } from '../init-flag-families.js';
+import { LIB_FLAGS, MOBILE_FLAGS, PIPELINE_FLAGS, ML_FLAGS, EXT_FLAGS, RESEARCH_FLAGS, applyFlagFamilyValidation, buildFlagOverrides, } from '../init-flag-families.js';
 import { asScaffoldError } from '../../utils/errors.js';
 import { configParseError, configNotObject } from '../../utils/errors.js';
 import { ExitCode } from '../../types/enums.js';
@@ -300,6 +300,26 @@ const adoptCommand = {
             .option('ext-background-worker', {
             type: 'boolean',
             describe: 'Background worker support',
+        })
+            // Research Configuration
+            .option('research-driver', {
+            type: 'string',
+            describe: 'Experiment driver',
+            choices: ['code-driven', 'config-driven', 'api-driven', 'notebook-driven'],
+        })
+            .option('research-interaction', {
+            type: 'string',
+            describe: 'Interaction mode',
+            choices: ['autonomous', 'checkpoint-gated', 'human-guided'],
+        })
+            .option('research-domain', {
+            type: 'string',
+            describe: 'Research domain',
+            choices: ['none', 'quant-finance', 'ml-research', 'simulation'],
+        })
+            .option('research-tracking', {
+            type: 'boolean',
+            describe: 'Experiment tracking',
         })
             // Game configuration options
             .option('engine', {
@@ -383,6 +403,7 @@ const adoptCommand = {
             .group([...PIPELINE_FLAGS], 'Data Pipeline Configuration:')
             .group([...ML_FLAGS], 'ML Configuration:')
             .group([...EXT_FLAGS], 'Browser Extension Configuration:')
+            .group([...RESEARCH_FLAGS], 'Research Configuration:')
             .group([
             'game-engine', 'game-multiplayer', 'game-target-platforms', 'game-online-services',
             'game-content-structure', 'game-economy', 'game-narrative', 'game-locales',

package/dist/cli/commands/adopt.js.map

@@ -1 +1 @@
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package/dist/cli/commands/adopt.serialization.test.js

@@ -74,6 +74,7 @@ vi.mock('../../project/adopt.js', () => ({
         ml: 'mlConfig',
         'browser-extension': 'browserExtensionConfig',
         game: 'gameConfig',
+        research: 'researchConfig',
     },
 }));
 vi.mock('../../core/assembly/meta-prompt-loader.js', () => ({
@@ -214,6 +215,46 @@ describe('adopt CLI JSON serialization', () => {
         expect(json.game_config).toEqual({ engine: 'unity' });
         expect(json.detected_config).toEqual({ type: 'game', config: { engine: 'unity' } });
     });
+    it('research detection roundtrips through JSON serialization', async () => {
+        vi.mocked(runAdoption).mockResolvedValueOnce({
+            mode: 'brownfield',
+            artifactsFound: 0,
+            detectedArtifacts: [],
+            stepsCompleted: [],
+            stepsRemaining: [],
+            methodology: 'deep',
+            errors: [],
+            warnings: [],
+            projectType: 'research',
+            detectedConfig: {
+                type: 'research',
+                config: {
+                    experimentDriver: 'code-driven',
+                    interactionMode: 'checkpoint-gated',
+                    hasExperimentTracking: true,
+                    domain: 'quant-finance',
+                },
+            },
+            detectionConfidence: 'high',
+            detectionEvidence: [{ signal: 'jupyter-notebooks', file: 'experiments/' }],
+        });
+        await adoptCommand.handler(defaultArgv());
+        const json = parseJsonOutput();
+        expect(json.project_type).toBe('research');
+        expect(json.detected_config).toEqual({
+            type: 'research',
+            config: {
+                experimentDriver: 'code-driven',
+                interactionMode: 'checkpoint-gated',
+                hasExperimentTracking: true,
+                domain: 'quant-finance',
+            },
+        });
+        expect(json.detection_confidence).toBe('high');
+        expect(json.detection_evidence).toEqual([
+            { signal: 'jupyter-notebooks', file: 'experiments/' },
+        ]);
+    });
     it('omits optional fields when not present', async () => {
         vi.mocked(runAdoption).mockResolvedValueOnce({
             mode: 'brownfield',

package/dist/cli/commands/adopt.serialization.test.js.map

@@ -1 +1 @@
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package/dist/cli/commands/init.d.ts

@@ -56,6 +56,10 @@ interface InitArgs {
     'ext-ui-surfaces'?: string[];
     'ext-content-script'?: boolean;
     'ext-background-worker'?: boolean;
+    'research-driver'?: string;
+    'research-interaction'?: string;
+    'research-domain'?: string;
+    'research-tracking'?: boolean;
 }
 declare const initCommand: CommandModule<Record<string, unknown>, InitArgs>;
 export default initCommand;

package/dist/cli/commands/init.d.ts.map

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

@@ -6,7 +6,7 @@ import { syncSkillsIfNeeded } from '../../core/skills/sync.js';
 import { shutdown } from '../shutdown.js';
 import { ProjectTypeSchema } from '../../config/schema.js';
 import { coerceCSV } from '../utils/coerce.js';
-import { GAME_FLAGS, WEB_FLAGS, BACKEND_FLAGS, CLI_TYPE_FLAGS, LIB_FLAGS, MOBILE_FLAGS, PIPELINE_FLAGS, ML_FLAGS, EXT_FLAGS, applyFlagFamilyValidation, } from '../init-flag-families.js';
+import { GAME_FLAGS, WEB_FLAGS, BACKEND_FLAGS, CLI_TYPE_FLAGS, LIB_FLAGS, MOBILE_FLAGS, PIPELINE_FLAGS, ML_FLAGS, EXT_FLAGS, RESEARCH_FLAGS, applyFlagFamilyValidation, } from '../init-flag-families.js';
 const initCommand = {
     command: 'init',
     describe: 'Initialize scaffold for this project',
@@ -220,6 +220,26 @@ const initCommand = {
             .option('ext-background-worker', {
             type: 'boolean',
             describe: 'Background worker support',
+        })
+            // Research Configuration
+            .option('research-driver', {
+            type: 'string',
+            describe: 'Experiment driver',
+            choices: ['code-driven', 'config-driven', 'api-driven', 'notebook-driven'],
+        })
+            .option('research-interaction', {
+            type: 'string',
+            describe: 'Interaction mode',
+            choices: ['autonomous', 'checkpoint-gated', 'human-guided'],
+        })
+            .option('research-domain', {
+            type: 'string',
+            describe: 'Research domain',
+            choices: ['none', 'quant-finance', 'ml-research', 'simulation'],
+        })
+            .option('research-tracking', {
+            type: 'boolean',
+            describe: 'Experiment tracking',
         })
             // Game configuration options
             .option('engine', {
@@ -326,6 +346,7 @@ const initCommand = {
             .group([...PIPELINE_FLAGS], 'Data Pipeline Configuration:')
             .group([...ML_FLAGS], 'ML Configuration:')
             .group([...EXT_FLAGS], 'Browser Extension Configuration:')
+            .group([...RESEARCH_FLAGS], 'Research Configuration:')
             .group([
             'game-engine', 'game-multiplayer', 'game-target-platforms', 'game-online-services',
             'game-content-structure', 'game-economy', 'game-narrative', 'game-locales',
@@ -347,6 +368,7 @@ const initCommand = {
         const hasPipelineFlag = PIPELINE_FLAGS.some((f) => argv[f] !== undefined);
         const hasMlFlag = ML_FLAGS.some((f) => argv[f] !== undefined);
         const hasExtFlag = EXT_FLAGS.some((f) => argv[f] !== undefined);
+        const hasResearchFlag = RESEARCH_FLAGS.some((f) => argv[f] !== undefined);
         const detectedType = hasGameFlag
             ? 'game'
             : hasWebFlag
@@ -365,7 +387,9 @@ const initCommand = {
                                         ? 'ml'
                                         : hasExtFlag
                                             ? 'browser-extension'
-                                            : undefined;
+                                            : hasResearchFlag
+                                                ? 'research'
+                                                : undefined;
         const projectType = argv['project-type'] ?? detectedType;
         let result;
         await shutdown.withContext('Cancelled. No changes were made.', async () => {
@@ -445,6 +469,12 @@ const initCommand = {
                     extContentScript: argv['ext-content-script'],
                     extBackgroundWorker: argv['ext-background-worker'],
                 } : undefined,
+                researchFlags: hasResearchFlag ? {
+                    researchDriver: argv['research-driver'],
+                    researchInteraction: argv['research-interaction'],
+                    researchDomain: argv['research-domain'],
+                    researchTracking: argv['research-tracking'],
+                } : undefined,
             }));
             if (!result.success) {
                 for (const err of result.errors) {