refactor: flatten phase/step numbering to sequential integers

- Worker phases: 0→1, 1→2, 1.5→3, 2a→4, 2→5, 2.5→6, 3→7, 4→8, 5c→9, 5→10, 5b→11, 6→12
- Plan steps: 0→1, 0.5→2, 0.6→3, 1→4, 1a→5, 1b→6, 2→7, 3→8, 4→9, 5→10, 5.5→11, 6→12, 6b→13, 7→14, 8→15
- Work orchestrator: Phase 1→Step 1, Phase 2→Step 2, 3a-3j→Steps 3-14, Phase 4→Step 15, Phase 5→Step 16
- Added migrate_phase_id() for backward-compat with old SQLite phase progress
- Updated all cross-references in markdown and codex mirrors

Tasks: fn-104.1 (Rust), fn-104.4 (Plan), fn-104.5 (Work)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: z23cc

codex/skills/flow-code-plan/SKILL.md

@@ -104,20 +104,20 @@ Research: repo-scout + rp(<mcp|cli|scout-fallback>) | Depth: <short|standard|dee
 ### Explicit flag overrides
 
 These flags override the corresponding AI decision without entering the analysis flow:
-- `--research=rp|grep`, `--depth=short|standard|deep`, `--review=rp|codex|export|none`, `--plan-only`, `--no-capability-scan` (skip capability-scout in Step 1)
-- `--interactive` — **opt-in** interview refinement. Before Context Analysis, invoke `/flow-code:interview` with the raw request text. The interview returns refined-spec markdown (Problem / Scope / Acceptance / Open Questions). Use that refined text as the effective request for Context Analysis and Step 1. When this flag is NOT passed, the plan flow is unchanged and the zero-interaction default (AGENTS.md:99) is preserved. There is intentionally no auto-trigger heuristic and no `--no-interview` flag — interview is opt-in only.
+- `--research=rp|grep`, `--depth=short|standard|deep`, `--review=rp|codex|export|none`, `--plan-only`, `--no-capability-scan` (skip capability-scout in Step 4)
+- `--interactive` — **opt-in** interview refinement. Before Context Analysis, invoke `/flow-code:interview` with the raw request text. The interview returns refined-spec markdown (Problem / Scope / Acceptance / Open Questions). Use that refined text as the effective request for Context Analysis and Step 4. When this flag is NOT passed, the plan flow is unchanged and the zero-interaction default (AGENTS.md:99) is preserved. There is intentionally no auto-trigger heuristic and no `--no-interview` flag — interview is opt-in only.
 
-Proceed to Step 1 immediately.
+Proceed to Step 4 immediately.
 
 ## Workflow
 
 Read [steps.md](steps.md) and follow each step in order.
 
-**CRITICAL — Step 1 (Research)**: You MUST launch ALL scouts listed in steps.md in ONE parallel Task call. Do NOT skip scouts or run them sequentially. Each scout provides unique signal.
+**CRITICAL — Step 4 (Research)**: You MUST launch ALL scouts listed in steps.md in ONE parallel Task call. Do NOT skip scouts or run them sequentially. Each scout provides unique signal.
 
 If review was decided (rp/codex/export):
-- rp or codex: run `/flow-code:plan-review` after Step 4, fix issues until it passes
-- export: run `/flow-code:plan-review` with export mode after Step 4
+- rp or codex: run `/flow-code:plan-review` after Step 9, fix issues until it passes
+- export: run `/flow-code:plan-review` with export mode after Step 9
 
 ## Output
 
@@ -135,9 +135,9 @@ All plans go into `.flow/`:
 
 ## Auto-Execute
 
-**Steps.md Step 8 handles auto-execution.** After steps complete:
-- Default: `/flow-code:work <epic-id> --no-review` invoked automatically (Step 8)
-- `--plan-only`: shows plan summary and stops (Step 8)
+**Steps.md Step 15 handles auto-execution.** After steps complete:
+- Default: `/flow-code:work <epic-id> --no-review` invoked automatically (Step 15)
+- `--plan-only`: shows plan summary and stops (Step 15)
 
 **After work completes** (if auto-executed):
 - All tasks done → Layer 3 adversarial review runs automatically (Phase 3j)

codex/skills/flow-code-plan/steps.md

@@ -1,6 +1,6 @@
 # Flow Plan Steps
 
-**IMPORTANT**: Steps 1-3 (research, gap analysis, depth) ALWAYS run regardless of input type.
+**IMPORTANT**: Steps 4-9 (research, gap analysis, depth) ALWAYS run regardless of input type.
 
 **CRITICAL**: If you are about to create:
 - a markdown TODO list,
@@ -34,7 +34,7 @@ Use **T-shirt sizes** based on observable metrics — not token estimates (model
 
 **Rules**: Combine sequential S tasks into one M. Split L tasks into M tasks. If 7+ tasks, look for over-splitting. Minimize file overlap between tasks for parallel work — list expected files in `**Files:**`, use `flowctl dep add` when tasks must share files.
 
-## Step 0: Initialize .flow
+## Step 1: Initialize .flow
 
 **CRITICAL: flowctl is BUNDLED — NOT installed globally.** `which flowctl` will fail (expected). Always use:
 
@@ -46,11 +46,11 @@ FLOWCTL="$HOME/.flow/bin/flowctl"
 $FLOWCTL init --json
 ```
 
-> **Note — opt-in interactive refinement:** If the user passed `--interactive`, BEFORE running Step 0 (Context Analysis in SKILL.md), invoke `/flow-code:interview` with the raw request text. The interview returns refined-spec markdown with Problem / Scope / Acceptance / Open Questions sections; use that refined text as the effective request for Context Analysis and all subsequent steps. Without the flag, skip this entirely — Step 0.5 below remains an automated internal brainstorm and is **not** interactive. Do not add any auto-trigger heuristic (length, punctuation, verb detection); interview must be opt-in only to preserve the zero-interaction contract (AGENTS.md:99).
+> **Note — opt-in interactive refinement:** If the user passed `--interactive`, BEFORE running Step 1 (Context Analysis in SKILL.md), invoke `/flow-code:interview` with the raw request text. The interview returns refined-spec markdown with Problem / Scope / Acceptance / Open Questions sections; use that refined text as the effective request for Context Analysis and all subsequent steps. Without the flag, skip this entirely — Step 2 below remains an automated internal brainstorm and is **not** interactive. Do not add any auto-trigger heuristic (length, punctuation, verb detection); interview must be opt-in only to preserve the zero-interaction contract (AGENTS.md:99).
 
-## Step 0.5: Clarity Check (auto — no human input)
+## Step 2: Clarity Check (auto — no human input)
 
-**Clear?** (specific behavior, bug with repro, existing pattern, has acceptance criteria) → skip to Step 1.
+**Clear?** (specific behavior, bug with repro, existing pattern, has acceptance criteria) → skip to Step 4.
 
 **Ambiguous?** (vague goal, multiple valid approaches, missing who/what/why, unclear scope) → mini brainstorm:
 
@@ -59,7 +59,7 @@ $FLOWCTL init --json
 3. Pick best by: blast radius, value/effort, codebase alignment
 4. Output: `Clarified: "<original>" → "<specific target>" | Approach: <A|B|C> — <why>`
 
-## Step 1: Fast research (parallel)
+## Step 4: Fast research (parallel)
 
 **If input is a Flow ID** (fn-N-slug or fn-N-slug.M, including legacy fn-N/fn-N-xxx): First fetch it with `$FLOWCTL show <id> --json` and `$FLOWCTL cat <id>` to get the request context.
 
@@ -103,9 +103,9 @@ Must capture:
 - Architecture patterns and data flow
 - Epic dependencies (from epic-scout)
 - Doc updates needed (from docs-gap-scout) - add to task acceptance criteria
-- Capability gaps (from capability-scout) - persist in Step 5 (see below)
+- Capability gaps (from capability-scout) - persist in Step 10 (see below)
 
-### Step 1a: Deep context via RP (after repo-scout)
+### Step 5: Deep context via RP (after repo-scout)
 
 After repo-scout returns, gather deep codebase context using the best available RP tier. **Exactly one RP-powered call per plan run** — do not call both context_builder and context-scout.
 
@@ -130,7 +130,7 @@ Run `context-scout` as a subagent (existing behavior, unchanged). This is the pr
 
 Feed RP/context-scout findings into the epic spec alongside repo-scout findings.
 
-## Step 1b: Apply memory lessons (if memory.enabled)
+## Step 6: Apply memory lessons (if memory.enabled)
 
 **Skip if memory.enabled is false.**
 
@@ -158,7 +158,7 @@ $FLOWCTL memory search "<keyword matching this plan's domain>"
 - If a past decision conflicts with the current plan, note it as an explicit "supersedes decision #N" in the epic spec
 - 0-3 applied entries per plan is normal
 
-## Step 2: Stakeholder & scope check
+## Step 7: Stakeholder & scope check
 
 Before diving into gaps, identify who's affected:
 - **End users** — What changes for them? New UI, changed behavior?
@@ -167,13 +167,13 @@ Before diving into gaps, identify who's affected:
 
 This shapes what the plan needs to cover.
 
-## Step 3: Flow gap check
+## Step 8: Flow gap check
 
 Run gap analyst subagent: `flow-code:flow-gap-analyst(<request>, research_findings)`. Fold gaps into the plan.
 
-**After epic is created (Step 5):** Register gaps via `$FLOWCTL gap add --epic <id> --capability "<desc>" --priority required|important|nice-to-have --source flow-gap-analyst --json`. Priority mapping: "MUST answer" → required, high-impact edge cases → important, deferrable → nice-to-have.
+**After epic is created (Step 10):** Register gaps via `$FLOWCTL gap add --epic <id> --capability "<desc>" --priority required|important|nice-to-have --source flow-gap-analyst --json`. Priority mapping: "MUST answer" → required, high-impact edge cases → important, deferrable → nice-to-have.
 
-## Step 4: Pick depth
+## Step 9: Pick depth
 
 Default to standard unless complexity demands more or less.
 
@@ -200,7 +200,7 @@ Default to standard unless complexity demands more or less.
 - Docs + metrics
 - Risks + mitigations
 
-## Step 5: Write to .flow
+## Step 10: Write to .flow
 
 **Efficiency note**: Use stdin (`--file -`) with heredocs to avoid temp files. Use `task spec` to set description + acceptance in one call.
 
@@ -332,7 +332,7 @@ Default to standard unless complexity demands more or less.
    - Max 5-7 targets per task — enough to ground the worker, not so many it wastes context
    - Use exact file paths with optional line ranges (e.g., `src/auth.ts:23-45`)
    - **Required** = must read before implementing. **Optional** = helpful reference
-   - Auto-populated from repo-scout/context-scout findings in Step 1 research
+   - Auto-populated from repo-scout/context-scout findings in Step 4 research
    - If no relevant files found by scouts, leave the section empty (worker skips Phase 1.5)
 
    **Layer field**: If stack config is set, tag each task with its primary layer. This helps the worker select the right guard commands (e.g., `pytest` for backend, `pnpm test` for frontend). Full-stack tasks run all guards.
@@ -356,7 +356,7 @@ Default to standard unless complexity demands more or less.
    $FLOWCTL cat <epic-id>
    ```
 
-## Step 5.5: Write capability-gaps.md (if capability-scout ran)
+## Step 11: Write capability-gaps.md (if capability-scout ran)
 
 **Skip if `--no-capability-scan` was passed, or capability-scout was not run, or scout errored (fails open).**
 
@@ -384,26 +384,26 @@ $FLOWCTL gap add --epic <epic-id> \
 
 `important` and `nice-to-have` gaps are recorded in the markdown file only — not in the gap registry (don't over-fill with noise).
 
-## Step 6: Validate
+## Step 12: Validate
 
 ```bash
 $FLOWCTL validate --epic <epic-id> --json
 ```
 
 Fix any errors before proceeding.
 
-### Step 6b: Auto-Extract Acceptance Checklist
+### Step 13: Auto-Extract Acceptance Checklist
 
 After validation, generate `.flow/checklists/<epic-id>.json` by parsing `## Acceptance` sections from epic + task specs. Each `- [ ]` line becomes a checklist item with `source` (epic or task ID) and `status: "pending"`. Skip if no acceptance criteria found. Commit with the plan (`git add .flow/checklists/`). Consumed by `/flow-code:epic-review`.
 
-## Step 7: Review (if chosen at start)
+## Step 14: Review (if chosen at start)
 
 If review was decided in Context Analysis:
 1. Initialize `PLAN_REVIEW_ITERATIONS=0`
 2. Invoke `/flow-code:plan-review` with the epic ID
 3. If review returns "Needs Work" or "Major Rethink":
    - Increment `PLAN_REVIEW_ITERATIONS`
-   - **If `PLAN_REVIEW_ITERATIONS >= 2`**: stop the loop. Log: "Plan review: 2 iterations completed. Proceeding." Go to Step 8.
+   - **If `PLAN_REVIEW_ITERATIONS >= 2`**: stop the loop. Log: "Plan review: 2 iterations completed. Proceeding." Go to Step 15.
    - **Re-anchor EVERY iteration** (do not skip):
      ```bash
      $FLOWCTL show <epic-id> --json
@@ -417,7 +417,7 @@ If review was decided in Context Analysis:
 
 **Why re-anchor every iteration?** Per Anthropic's long-running agent guidance: context compresses, you forget details. Re-read before each fix pass.
 
-## Step 8: Execute or Offer next steps
+## Step 15: Execute or Offer next steps
 
 **If `--plan-only`**: print `Plan created: <epic-id> (N tasks) | Next: /flow-code:work <epic-id>` and stop.
 

codex/skills/flow-code-work/SKILL.md

@@ -69,8 +69,8 @@ REVIEW_BACKEND=$($FLOWCTL review-backend)
 Based on context, decide:
 - **Branch**: on feature branch → stay (`current`). on main/master → create worktree (`worktree`). dirty working tree → `current`.
 - **Per-task review**: `none` by default. Three-layer quality system handles review at the right levels:
-  - Layer 1 (guard): runs per-commit in worker Phase 2.5 — always on
-  - Layer 3 (codex adversarial): runs at epic completion in Phase 3j — auto-detects codex CLI
+  - Layer 1 (guard): runs per-commit in Worker Phase 6 — always on
+  - Layer 3 (codex adversarial): runs at epic completion in Step 14 — auto-detects codex CLI
   - Per-task Codex/RP review only if explicitly requested via `--review=rp|codex`
 
 Output one line: