chore: remove all deprecated skill references from docs [fn-16]

Clean up remaining "deprecated" annotations and stale references to
deleted skills (plan, work, plan-review, impl-review, epic-review).
CLAUDE.md, docs/skills.md, docs/CODEBASE_MAP.md, agents/worker.md
now reference only flow-code-run as the primary entry point.

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

Author: z23cc

CLAUDE.md

@@ -18,7 +18,7 @@ hooks/hooks.json         → Ralph workflow guards (active when FLOW_RALPH=1)
 docs/                    → Architecture docs, CI examples
 ```
 
-**Skills**: 9 core + 22 extensions. See `docs/skills.md` for the full classification. Core workflow: `flow-code-run` (unified phase loop). Legacy individual skills (plan, plan-review, work, impl-review, epic-review) are deprecated but still functional as thin redirects.
+**Skills**: See `docs/skills.md` for the full classification. Core workflow: `flow-code-run` (unified phase loop via `flowctl phase next/done`).
 
 **Key invariant**: The `bin/flowctl` Rust binary is the single source of truth for `.flow/` state. Always invoke as:
 ```bash
@@ -28,14 +28,7 @@ $FLOWCTL <command>
 
 ## Primary Workflow
 
-**Unified entry point** (preferred): `/flow-code:run "description"` — drives the entire pipeline (plan → plan-review → work → impl-review → close) via `flowctl phase next/done`. One command, zero manual phase transitions.
-
-Individual phase commands (deprecated, still functional):
-1. `/flow-code:plan "description"` → creates epic + tasks in `.flow/`
-2. `/flow-code:plan-review` → Carmack-level review via RepoPrompt or Codex
-3. `/flow-code:work <epic-id>` → executes tasks with Teams mode (auto-parallel with file locking)
-4. `/flow-code:impl-review` → post-implementation review
-5. `/flow-code:epic-review` → final review before closing
+`/flow-code:run "description"` — drives the entire pipeline (plan → plan-review → work → impl-review → close) via `flowctl phase next/done`. One command, zero manual phase transitions.
 
 Ralph (`/flow-code:ralph-init`) is the autonomous harness that runs this loop unattended.
 

agents/worker.md

@@ -1,6 +1,6 @@
 ---
 name: worker
-description: Task implementation worker. Spawned by flow-code-work to implement a single task with fresh context. Do not invoke directly - use /flow-code:work instead.
+description: Task implementation worker. Spawned by flow-code-run during the work phase. Do not invoke directly - use /flow-code:run instead.
 model: inherit
 disallowedTools: Task
 color: "#3B82F6"

docs/CODEBASE_MAP.md

@@ -110,13 +110,9 @@ flow-code/
 │   ├── setup.md, sync.md, uninstall.md
 ├── skills/                       # 18 skill implementations
 │   ├── flow-code/                # Task CRUD via flowctl
-│   ├── flow-code-plan/           # SKILL.md + steps.md + examples.md
-│   ├── flow-code-work/           # SKILL.md + phases.md
+│   ├── flow-code-run/            # Unified pipeline entry point (phase loop)
 │   ├── flow-code-interview/      # SKILL.md + questions.md
 │   ├── flow-code-prime/          # SKILL.md + workflow.md + pillars.md + remediation.md
-│   ├── flow-code-impl-review/    # SKILL.md + workflow.md + flowctl-reference.md
-│   ├── flow-code-plan-review/    # SKILL.md + workflow.md + flowctl-reference.md
-│   ├── flow-code-epic-review/    # SKILL.md + workflow.md + flowctl-reference.md
 │   ├── flow-code-ralph-init/     # SKILL.md + templates/ (ralph.sh, config.env, prompts)
 │   ├── flow-code-auto-improve/   # SKILL.md + templates/ (auto-improve.sh, programs/)
 │   ├── flow-code-map/            # SKILL.md + scripts/scan-codebase.py
@@ -246,24 +242,21 @@ sequenceDiagram
     Interview->>flowctl: epic set-plan (refined spec)
 
     Note over User,flowctl: Preferred: /flow-code:run fn-N (unified pipeline)
-    Note over User,flowctl: Legacy individual commands (deprecated, still functional):
-    User->>Plan: /flow-code:plan fn-N
-    Plan->>Scouts: 7 scouts in parallel
-    Scouts-->>Plan: patterns, docs, gaps, deps
-    Plan->>flowctl: epic create + task create (with deps)
-
-    User->>Work: /flow-code:work fn-N
-    loop Each ready task
-        Work->>flowctl: start task
-        Work->>Worker: spawn (fresh context)
-        Worker->>flowctl: show + cat (re-anchor)
-        Worker->>Worker: implement + test + commit
-        Worker->>Review: impl-review (if enabled)
-        Review-->>Worker: SHIP / NEEDS_WORK (fix loop)
-        Worker->>flowctl: done (summary + evidence)
+    User->>Run: /flow-code:run "description"
+    loop flowctl phase next/done
+        Run->>flowctl: phase next --epic fn-N --json
+        flowctl-->>Run: {phase, prompt, all_done}
+        alt phase = plan
+            Run->>Scouts: research scouts in parallel
+            Scouts-->>Run: patterns, docs, gaps
+            Run->>flowctl: epic plan + task create
+        else phase = work
+            Run->>Worker: spawn workers (Teams + worktree)
+            Worker->>flowctl: worker-phase next/done loop
+            Worker->>flowctl: done (summary + evidence)
+        end
+        Run->>flowctl: phase done --epic fn-N --phase X
     end
-    Work->>Review: epic-review (completion gate)
-    Review-->>Work: SHIP
 ```
 
 ### Ralph Autonomous Loop
@@ -279,13 +272,13 @@ sequenceDiagram
 
     alt status = plan
         ralph.sh->>Claude: prompt_plan.md (new process)
-        Claude->>Claude: /flow-code:plan-review (deprecated, handled by run pipeline)
+        Claude->>Claude: /flow-code:run (plan phase)
     else status = work
         ralph.sh->>Claude: prompt_work.md (new process)
-        Claude->>Claude: /flow-code:work + impl-review (deprecated, handled by run pipeline)
+        Claude->>Claude: /flow-code:run (work phase)
     else status = completion_review
         ralph.sh->>Claude: prompt_completion.md (new process)
-        Claude->>Claude: /flow-code:epic-review (deprecated, handled by run pipeline)
+        Claude->>Claude: /flow-code:run (close phase)
     end
 
     Claude-->>ralph.sh: exit (verdict in log)
@@ -342,9 +335,9 @@ sequenceDiagram
 
 **To add a new command**: Create `commands/flow-code/<name>.md` (thin stub) + `skills/flow-code-<name>/SKILL.md`
 **To add a new agent**: Create `agents/<name>.md` with frontmatter (name, description, model, disallowedTools)
-**To add a new scout to planning**: Add to the parallel scout list in `skills/flow-code-plan/steps.md` Step 1
+**To add a new scout to planning**: Add to the scout dispatch in `skills/flow-code-run/SKILL.md` plan phase
 **To add a new prime pillar**: Add criteria to `skills/flow-code-prime/pillars.md`, remediation to `remediation.md`
 **To modify Ralph loop**: Edit `skills/flow-code-ralph-init/templates/ralph.sh` (canonical source)
 **To modify auto-improve loop**: Edit `skills/flow-code-auto-improve/templates/auto-improve.sh`
-**To add a review backend**: Add to impl-review, plan-review, and epic-review workflow.md files
-**To change task state machine**: Modify `scripts/flowctl/commands/workflow.py` (state transitions) or `scripts/flowctl/core/state.py` (state storage)
+**To add a review backend**: Add to `flowctl review-backend` and the review phase in `skills/flow-code-run/SKILL.md`
+**To change task state machine**: Modify `flowctl/crates/flowctl-core/src/state_machine.rs`

docs/skills.md

@@ -2,19 +2,14 @@
 
 Skills are organized into **core** (essential workflow) and **extensions** (optional capabilities).
 
-## Core Skills (9)
+## Core Skills (4)
 
-These skills form the primary plan-execute-review workflow. They ship with the plugin.
+These skills form the primary workflow. They ship with the plugin.
 
 | Skill | Command | Purpose |
 |-------|---------|---------|
 | `flow-code-run` | `/flow-code:run` | **Primary entry point** — unified phase loop (plan → review → work → close) |
 | `flow-code` | `/flow-code` | Task/epic management entry point (list, create, status) |
-| `flow-code-plan` | `/flow-code:plan` | Create structured build plans (deprecated — use `run`) |
-| `flow-code-work` | `/flow-code:work` | Execute plans with Teams mode (deprecated — use `run`) |
-| `flow-code-plan-review` | `/flow-code:plan-review` | Carmack-level plan review (deprecated — use `run`) |
-| `flow-code-impl-review` | `/flow-code:impl-review` | Post-implementation code review (deprecated — use `run`) |
-| `flow-code-epic-review` | `/flow-code:epic-review` | Final review before closing (deprecated — use `run`) |
 | `flow-code-setup` | `/flow-code:setup` | Install flowctl CLI and configure project |
 | `flow-code-map` | `/flow-code:map` | Generate codebase architecture maps |
 
@@ -67,5 +62,4 @@ For a new project:
 2. `/flow-code:prime` — assess codebase readiness
 3. `/flow-code:run "description"` — plan, review, execute, and close (all-in-one)
 
-Legacy individual commands (deprecated, still functional):
-3a. `/flow-code:plan "description"` → 4. `/flow-code:plan-review` → 5. `/flow-code:work <epic-id>` → 6. `/flow-code:impl-review` → 7. `/flow-code:epic-review`
+That's it — `/flow-code:run` handles the full plan → review → work → review → close pipeline.