chore(cli)!: remove `--stacked`, `--reflect` and `--full-qa` — flags, `run.fullQa`, the MCP `fullQa` parameter and `run-reflect.ts`; `--chain` keeps working

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Refactor
Clarity
Clearly specified
Activity status
Active
Tech stack
node.js, typescript
Domain
cli, developer-experience

Research direction

Start with #1647, which blocks this issue and edits several of the same files. Then trace the named surfaces in bin/cli.ts, src/lib/settings.ts, src/mcp/tools/run.ts, src/commands/run.ts, and the workflow files; use the listed acceptance commands to check each removal and confirm --chain still works. Done means all eight acceptance criteria pass, including the changelog update.

Written by the indexing model from the issue text.

Description

graph-2026-11-simplify

Epic: graph-2026-11-simplify (F-10 cluster of #1501) Tier: mechanical Execution: sequant_run Blocked by: #1647 (both edit bin/cli.ts, KNOWN_KEYS in settings.ts, types.ts and src/commands/run.ts)

  • Blocked by: #1647

Problem

D-1. In 453 recorded runs --stacked, --reflect and --full-qa were each used 0 times. --reflect is read once (run-display.ts:297) and calls run-reflect.ts (291 lines). --stacked implies --chain (run.ts:67-74) and threads a predecessor base through worktree-manager.ts and batch-executor.ts:1406. --full-qa exists as a flag, the run.fullQa setting (#982) and a fullQa parameter on MCP sequant_run (src/mcp/tools/run.ts:655). D-3 keeps --chain, so the stacked-only paths go and the chain paths stay. Founding doc §4, OQ-1.

Decisions

ID Decision Rejected
X-1 ExecutionConfig.fullQa (#683) stays: sequant ready forces it on every gate pass (settings.ts:383-389). Only the opt-in surfaces go: --full-qa, run.fullQa, the MCP fullQa parameter removing the config field (breaks sequant ready)
X-2 The MCP input schema strips unknown keys (no .strict() in src/mcp/tools/run.ts), so a caller still passing fullQa is ignored, not refused. OQ-1's grep is the check; no new warning surface a strict schema for one removed key

Prior fixes / producers

  • Prior removals: #503–#508. --stacked landed in #605; --full-qa in #982.
  • Producers: bin/cli.ts, src/lib/settings.ts (KNOWN_KEYS.run, schema, generated table), src/mcp/tools/run.ts, src/commands/run.ts, src/commands/run-display.ts, src/lib/workflow/{types,batch-executor,worktree-manager,run-reflect}.ts, docs/reference/run-command.md, docs/features/. Class: outcome per named surface.

Acceptance Criteria

  • AC-1: None of the three flags appears on run or ready. Evidence: for c in run ready; do npx tsx bin/cli.ts $c --help; done | grep -cE -- '--stacked|--reflect|--full-qa' → 0
  • AC-2: run-reflect.ts is gone and nothing imports it. Evidence: grep -rl 'run-reflect' src bin --include='*.ts' | wc -l | tr -d ' ' → 0
  • AC-3: The MCP tool no longer accepts fullQa and the setting is gone. Evidence: grep -c 'fullQa' src/mcp/tools/run.ts src/lib/settings.ts | awk -F: '{s+=$2} END{print s}' → 0
  • AC-4: A settings file that sets run.fullQa loads with one warning naming the removal in 3.0. Evidence: npx vitest run src/lib/settings.removed-keys.test.ts -t "fullQa" → ≥ 1 passed, 0 failed
  • AC-5: --chain still provisions, rebases and resumes. Evidence: npx vitest run src/lib/workflow/chain-preflight.test.ts src/lib/workflow/chain-resume.test.ts src/lib/workflow/chain-rebase.integration.test.ts → 0 failed (constraint)
  • AC-6: User docs no longer offer them. Evidence: grep -rlE -- '--stacked|--reflect|--full-qa|fullQa' README.md docs/reference docs/features docs/guides docs/getting-started | wc -l | tr -d ' ' → 0
  • AC-7: The changelog records the removal. Evidence: awk '/^## \[Unreleased\]/,/^## \[[0-9]/' CHANGELOG.md | grep -cE -- '--stacked|--reflect|--full-qa' → ≥ 1
  • AC-8: No skill-directory edits. Evidence: git diff --name-only $(git merge-base origin/main HEAD)..HEAD | grep -cE '^(plugin/|\.claude/skills/|templates/skills/)' → 0 (constraint)

OQ-1 (does any MCP caller pass fullQa): exec greps ~/Projects/harness and docs/internal/graph-*/HANDOFF.md and records the count in the PR body; no AC depends on it.

May touch

bin/cli.ts (the three .option( blocks only), src/lib/settings.ts, src/mcp/tools/run.ts and test, src/commands/run.ts, src/commands/run-display.ts, src/lib/workflow/run-reflect.ts and test (deleted), full-qa.test.ts (deleted), types.ts, batch-executor.ts and worktree-manager.ts (stacked branches only), their tests, docs/reference/run-command.md (flag rows only), CHANGELOG.

Non-Goals

  • The /reflect skill text (frozen; §10).
  • --chain, multi-issue runs (#1651), sequant ready.

Done when

No flag, setting, MCP parameter or user doc offers stacked PRs, reflection or full-weight QA, and the chain suite is green.

Dominant language
TypeScript
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Forks
1
Avg merge
11h 3m
Merged PRs (30d)
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