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69c4b31
chore: update .STATUS with v5.15.1 release and future documentation p…
Jan 22, 2026
1f337a0
docs(specs): add documentation debt remediation spec
Jan 22, 2026
5f0e010
chore: update .STATUS with documentation-debt worktree and spec
Jan 22, 2026
210b7a0
docs: update CLAUDE.md for v5.15.1
Jan 22, 2026
945bec8
docs: Phase 1 documentation debt - Core libraries (47 functions)
Jan 22, 2026
de4070b
fix(docs): correct anchor links in CORE-API-REFERENCE.md
Jan 22, 2026
b476f20
chore: merge main (prettier 3.8.0)
Jan 22, 2026
f10f862
feat: implement teach analyze Phase 0 - concept extraction and prereq…
Jan 22, 2026
5da4491
fix: correct concept display formatting in teach analyze output
Jan 22, 2026
b2ff1b8
feat(Phase 1): integrate concept validation with teach validate and s…
Jan 22, 2026
7063811
feat(Phase 1): add concepts schema and templates
Jan 22, 2026
40549e5
test: add Phase 1 unit tests for teach analyze
Jan 22, 2026
e55fe8e
docs: add Intelligent Content Analysis user guide
Jan 22, 2026
1bf18bf
fix: resolve variable conflicts in teach analyze loading
Jan 22, 2026
b6e5e80
chore: update .STATUS with Phase 1 completion
Jan 22, 2026
e48760a
chore: update .STATUS with Phase 2 planning
Jan 22, 2026
e6034b3
feat: Intelligent Content Analysis Phase 2
Jan 22, 2026
a4bc880
docs: add API reference for teach analyze Phase 2
Jan 22, 2026
86bd618
test: add Phase 2 integration tests (20 tests)
Jan 22, 2026
51ad31e
docs: complete documentation debt remediation (Phases 1-4)
Data-Wise Jan 22, 2026
5bd73b5
feat: add Phase 3 AI-powered analysis (--ai flag)
Jan 22, 2026
8596323
feat: add Phase 4 slide optimization (--slide-breaks, --optimize)
Jan 22, 2026
76d1f16
feat: add Phase 5 error handling, caching, and final tests (33 tests)
Jan 22, 2026
e0b4c64
docs: update teach analyze docs for Phases 3-5
Jan 22, 2026
13d9682
docs: add teach analyze quick reference card
Jan 22, 2026
dbf8d15
feat: wire up slides --key-concepts and auto-analyze integration
Jan 22, 2026
b0d3956
chore: update plugin comment to reflect Phase 0-5 completion
Jan 22, 2026
6cc3871
test: add slides --optimize integration tests (29 tests)
Jan 22, 2026
2234a8b
chore: update .STATUS - cleanup completed PRs and worktrees
Jan 22, 2026
65276e0
chore: mark teach analyze Phase 0 as in progress
Jan 22, 2026
903462a
docs: update changelog and fix mkdocs navigation
Jan 22, 2026
9ad6263
docs: add architecture diagrams and enhance API reference
Jan 22, 2026
093a66b
docs: add teach analyze interactive tutorial (10 steps)
Jan 22, 2026
cf48d02
chore: update project status and navigation for teach-analyze
Jan 22, 2026
2501899
chore: session wrap-up - cleanup and status update
Jan 23, 2026
26223ff
Merge remote-tracking branch 'origin/dev' into feature/teach-analyze
Jan 23, 2026
d84519c
Merge pull request #289 from Data-Wise/feature/teach-analyze
Data-Wise Jan 23, 2026
c0c04c9
refactor: optimize teach analyze sourcing and file structure (#290)
Data-Wise Jan 23, 2026
72b26e4
fix: wt dispatcher passthrough for lock/unlock/repair
Jan 23, 2026
92abfb4
fix: add 30s timeout to test runner to prevent hangs
Jan 23, 2026
05f2bf4
docs: document expected timeouts in test runner
Jan 23, 2026
6edd2df
docs: add plugin optimization tutorial and reference
Jan 23, 2026
7d9a4a7
docs: update site for v5.16.0 release
Jan 23, 2026
4eab6d9
test: add plugin optimization test suite (PR #290)
Jan 23, 2026
fac8184
docs: update test count to 393 (362 + 31 optimization tests)
Jan 23, 2026
043262d
docs: add comprehensive testing summary for v5.16.0
Jan 23, 2026
796baa8
test: add E2E and interactive dog feeding tests with demo course
Jan 23, 2026
ad4d4c5
test: extend E2E suite with Section 8 (4 new tests)
Jan 23, 2026
0cc9517
docs: update CLAUDE.md with E2E test infrastructure
Jan 23, 2026
994c67e
docs: update CHANGELOG with E2E test infrastructure
Jan 23, 2026
395c57a
fix: replace Unicode bullet with ASCII asterisk in interactive test
Jan 23, 2026
91d34d9
test: add diagnostic script to capture teach analyze outputs
Jan 23, 2026
aa0b9cf
fix: concept extraction now supports array-of-objects YAML format
Jan 23, 2026
4b7cec8
fix(teach analyze): convert relative paths to absolute for correct co…
Jan 23, 2026
0e10fa1
test: update interactive dog feeding test expectations
Jan 23, 2026
781dd18
fix(teach analyze): display prerequisites correctly by handling quote…
Jan 23, 2026
3c7e4b8
fix(slide optimizer): extract key concepts from actual concept graph …
Jan 23, 2026
db2f57e
feat(teach analyze): enhance prerequisites display with dependency tree
Jan 23, 2026
14c1b80
fix(concept extraction): process each concept individually to prevent…
Jan 23, 2026
0b2b108
docs(teach analyze): document enhanced prerequisite display
Jan 23, 2026
14a65c8
chore: bump version to 5.16.0
Jan 23, 2026
27965bb
chore: update .STATUS for v5.16.0 release
Jan 23, 2026
ebc7303
docs: update CLAUDE.md for v5.16.0 release
Jan 23, 2026
c138f9a
docs: add GitHub token automation spec
Jan 23, 2026
ecbd4f7
feat(dot): add token expiration detection
Jan 23, 2026
1d9f0d3
feat(dot): track token metadata in Keychain
Jan 23, 2026
7822112
feat(dot): add semi-automated token rotation
Jan 23, 2026
2404a5c
feat(dot): add gh CLI auto-sync
Jan 23, 2026
cd24fea
docs: add token health check guide
Jan 23, 2026
4737c91
feat(g): add token validation before remote ops
Jan 23, 2026
acc1a3c
feat(dash): add GitHub token status to dev dashboard
Jan 23, 2026
85d3c8d
feat(work): show token status in session banner
Jan 23, 2026
48f5cdc
feat(finish): validate token before push
Jan 23, 2026
4ac6adb
feat(flow): add token health checks to flow doctor
Jan 23, 2026
e2a3639
feat(flow): add flow token alias for dot token
Jan 23, 2026
fab381e
docs: add token automation to CLAUDE.md
Jan 23, 2026
10b1ab5
docs: add token automation to DOT reference
Jan 23, 2026
c89c005
test: add comprehensive token automation test suite
Jan 23, 2026
81c15f8
test: add comprehensive test suites for token automation
Jan 23, 2026
083ee63
fix(dot): wire up token automation subcommands
Jan 23, 2026
40690c2
docs(spec): approve Phase 1 for implementation, defer Phases 2-4
Jan 23, 2026
10b8bfd
test: fix failing tests and add comprehensive E2E suite
Jan 23, 2026
108c26f
docs: add Phase 1 completion summary
Jan 23, 2026
e339fb2
docs: complete Phase 1 token automation documentation
Jan 23, 2026
e1b7bce
docs: add pre-flight validation summary
Jan 23, 2026
e467304
Merge pull request #292 from Data-Wise/feature/token-automation
Data-Wise Jan 23, 2026
338d0bd
docs: update for v5.17.0 token automation merge
Jan 23, 2026
2700f6c
docs(site): update for v5.17.0 token automation
Jan 23, 2026
0e077df
docs(tutorial): add Tutorial 23 - Token Automation
Jan 23, 2026
0764663
Merge remote-tracking branch 'origin/main' into dev
Jan 23, 2026
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116 changes: 87 additions & 29 deletions .STATUS
Original file line number Diff line number Diff line change
Expand Up @@ -4,52 +4,95 @@
## Project: flow-cli
## Type: zsh-plugin
## Status: active
## Phase: v5.16.0 - In Development
## Phase: v5.17.0 - Planning
## Priority: 1
## Progress: 60
## Progress: 0

## Focus: Intelligent Content Analysis (teach analyze)
## Focus: Next Development Cycle

## βœ… Just Completed (2026-01-22):
## βœ… Just Released (2026-01-22):

### teach analyze - ALL PHASES COMPLETE + Optimized
### v5.16.0 - Intelligent Content Analysis ✨

**PR #289:** Merged to dev (Phases 0-5: concept extraction, caching, reports, AI, slides, polish)
**PR #290:** Merged to dev (post-merge optimization)
**Released:** 2026-01-22
**PR #291:** https://github.com/Data-Wise/flow-cli/pull/291
**Release:** https://github.com/Data-Wise/flow-cli/releases/tag/v5.16.0

**Optimization (PR #290):**
- Added self-protecting load guards to 6 lib files (prevents double/triple-sourcing)
- Extracted display layer to `lib/analysis-display.zsh` (7 functions, 270 lines)
- Fixed slide cache path collisions (directory-mirroring structure)
- Removed redundant sources from `flow.plugin.zsh` and dispatcher
**Major Features:**
- teach analyze system (Phases 0-5) - Complete intelligent content analysis with AI
- Plugin optimization (load guards, display extraction, cache fixes)
- Documentation debt remediation (348 functions, 49.4% coverage)
- Enhanced prerequisite display with dependency tree
- wt dispatcher passthrough fix
- 58 commits, 39,228 additions, 1,750 deletions

**Included PRs:**
- PR #289: teach analyze Phases 0-5
- PR #290: Plugin optimization
- PR #288: Documentation debt remediation

---

## 🎯 Current Sprint:

**Brainstorm:** Config→concept graph integration (Option D: Hybrid Enrichment for Phase 1)
**Spec:** `docs/specs/SPEC-teach-analyze-optimization-2026-01-22.md`
### v5.17.0 - Token Automation Phase 1 βœ… COMPLETE

### Bug Fix: wt dispatcher passthrough
**PR #292:** https://github.com/Data-Wise/flow-cli/pull/292 (MERGED 2026-01-23)
**Status:** Complete, merged to dev
**Time:** 8 hours (33% faster than 12h estimate via orchestration)

- `wt lock/unlock/repair` now correctly passes through to `git worktree`
- Added `lock|unlock|repair` to known commands list
**Delivered:**
- βœ… Isolated token checks (--dot, --dot=TOKEN)
- βœ… Smart caching (5-min TTL, 80% API reduction)
- βœ… ADHD-friendly category menu
- βœ… Verbosity levels (quiet/normal/verbose)
- βœ… Token-only fix mode (--fix-token)
- 1,822 lines code, 2,150+ lines docs, 54 tests (96.3% pass)

---

## 🎯 Current Sprint:
### v5.18.0 - GitHub Token Security & Automation (Future)

### v5.16.0 - Bundling for Release
**Status:** Deferred (focus on other features)
**Estimated:** 4 hours (1.5h Phase 1 + 2h Phase 2 + 0.5h testing)

**On dev (ready for release):**
- teach analyze (Phases 0-5) β€” full concept graph + AI + slide optimization
- teach analyze optimization (load guards, display extraction, cache fix)
- Documentation debt (348 functions documented, 49.4% coverage)
- wt dispatcher passthrough fix
**Features:**
- πŸ” Semi-automated GitHub token rotation with keychain integration
- ⏰ Token expiration detection (7-day warning at 83 days)
- πŸ”„ One-command token lifecycle (detection β†’ rotation β†’ validation β†’ revocation)
- 🎯 Integration across 9 dispatchers (g, dash, work, finish, teach, doctor, gh CLI, git, MCP)
- πŸ“Š Weekly health checks with audit trail

**Implementation Plan:**
- Phase 1 (1.5h): Core automation - 5 tasks
- Phase 2 (2h): flow-cli integration - 6 tasks
- Documentation: 0.5h

**Brainstorm Docs:**
- `~/BRAINSTORM-github-token-security-2026-01-23.md` (19KB)
- `~/BRAINSTORM-automated-token-management-2026-01-23.md` (36KB)
- `~/BRAINSTORM-flow-github-integration-2026-01-23.md` (22KB)

**Implementation Plan:**
- `~/.git-worktrees/flow-cli/feature-token-automation/IMPLEMENTATION-PLAN.md`

---

### v5.17.0 - Planning Phase (Paused)

**Potential Focus Areas (deferred):**
- Config β†’ concept graph integration (Phase 1 enhancement)
- teach prompt command (needs Scholar coordination)
- Quarto workflow Phase 2 enhancements
- Additional teach analyze improvements

---

## πŸ—‚οΈ Active Worktrees:

| Worktree | Branch | Status |
|----------|--------|--------|
| Main repo | `dev` | Planning/coordination |
| Main repo | `dev` | Clean - PR #292 merged |

---

Expand Down Expand Up @@ -78,7 +121,13 @@
- v5.15.1 (2026-01-21): Architecture docs, V-dispatcher reference, coverage report
- v5.15.0 (2026-01-21): Comprehensive Help System (18 functions, 3 guides)

**Future (v5.17.0+):**
**v5.18.0 (In Progress):**
- GitHub token security & automation ← ACTIVE
- Semi-automated rotation with keychain
- 9-dispatcher integration (g, dash, work, finish, etc.)
- Token expiration detection (7-day warning)

**Future (v5.19.0+):**
- Config→concept graph integration (Phase 1)
- teach analyze AI improvements
- Quarto Workflow Phase 2 (already on dev via PR #279)
Expand All @@ -87,12 +136,21 @@

## 🎯 Recommended Next Step:

Release v5.16.0 (dev → main) or start config→concept graph Phase 1.
**Immediate:** Release v5.17.0
- PR #292 merged to dev
- Run full test suite
- Create release PR (dev β†’ main)
- Tag v5.17.0

**After v5.17.0:** Choose next focus:
- Config→concept graph integration (Phase 1)
- teach analyze AI improvements
- v5.18.0 token automation (Phases 2-4)

---

**Last Updated:** 2026-01-23
**Status:** Active - v5.16.0 ready for release
**Status:** Active - v5.16.0 released, implementing v5.18.0 (token automation)
## wins: --category fix squashed the bug (2026-01-22), fixed the bug (2026-01-22), --category fix squashed the bug (2026-01-22), fixed the bug (2026-01-22), --category fix squashed the bug (2026-01-22)
## streak: 0
## last_active: 2026-01-22 22:26
## last_active: 2026-01-23 04:15
Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@ Implemented a comprehensive cache management system for the flow-cli Quarto teac
Core utilities for freeze cache management:

- **`_cache_status()`** - Get cache size, file count, last render time
- **`_cache_clear()`** - Delete _freeze/ with confirmation
- **`_cache_clear()`** - Delete \_freeze/ with confirmation
- **`_cache_rebuild()`** - Force full re-render (clear + quarto render)
- **`_cache_analyze()`** - Detailed breakdown by directory/age
- **`_cache_clean()`** - Delete both _freeze/ and _site/
- **`_cache_clean()`** - Delete both \_freeze/ and \_site/
- **Helper functions:**
- `_cache_format_time_ago()` - Human-readable time (e.g., "2 hours ago")
- `_cache_format_bytes()` - Convert bytes to KB/MB/GB
Expand All @@ -34,7 +34,7 @@ Interactive cache management interface:
- `teach cache clear [--force]` - Delete cache with confirmation
- `teach cache rebuild` - Clear and re-render
- `teach cache analyze` - Detailed breakdown
- **`teach_clean()`** - Standalone command to delete _freeze/ + _site/
- **`teach_clean()`** - Standalone command to delete \_freeze/ + \_site/
- **Complete help system** with examples

### 3. `tests/test-teach-cache-unit.zsh` (520 lines)
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ Successfully implemented comprehensive health check system for flow-cli's teachi
### 3. Documentation βœ…

**Files:**

- `docs/teach-doctor-implementation.md` (450+ lines) - Complete guide
- `TEACH-DOCTOR-SUMMARY.md` (200+ lines) - Implementation summary
- `IMPLEMENTATION-COMPLETE.md` (this file) - Final deliverable summary
Expand All @@ -60,23 +61,27 @@ Successfully implemented comprehensive health check system for flow-cli's teachi
βœ… **Goal:** Comprehensive health check with interactive fix

βœ… **Files to create:**

- `lib/doctor-helpers.zsh` - βœ… Implemented (as teach-doctor-impl.zsh)
- `commands/teach-doctor.zsh` - βœ… Integrated in teach dispatcher

βœ… **Health Checks:**

- `teach doctor` - βœ… Full health check
- `teach doctor --fix` - βœ… Interactive fix
- `teach doctor --json` - βœ… JSON output for CI
- `teach doctor --quiet` - βœ… Minimal output

βœ… **Checks Performed:**

1. βœ… Dependencies (Quarto, Git, yq, R packages, extensions)
2. βœ… Git setup (repository, remote, branches)
3. βœ… Project config (teaching.yml, _quarto.yml, freeze)
3. βœ… Project config (teaching.yml, \_quarto.yml, freeze)
4. βœ… Hook status (installed, version)
5. βœ… Cache health (_freeze/ size, last render)
5. βœ… Cache health (\_freeze/ size, last render)

βœ… **Interactive Fix:**

```bash
β”‚ βœ— yq not found
β”‚ Install via Homebrew? [Y/n] y
Expand All @@ -90,6 +95,7 @@ Successfully implemented comprehensive health check system for flow-cli's teachi
```

βœ… **Testing:**

- `tests/test-teach-doctor-unit.zsh` - βœ… 39 tests (100% passing)
- Mock missing dependencies - βœ… Implemented
- Test interactive fix prompts - βœ… Implemented
Expand All @@ -100,24 +106,24 @@ Successfully implemented comprehensive health check system for flow-cli's teachi

## Feature Matrix

| Feature | Specified | Implemented | Tested |
|---------|-----------|-------------|--------|
| Basic health check | βœ… | βœ… | βœ… |
| --quiet flag | βœ… | βœ… | βœ… |
| --fix flag | βœ… | βœ… | βœ… |
| --json flag | βœ… | βœ… | βœ… |
| --help flag | βœ… | βœ… | βœ… |
| Dependency checks | βœ… | βœ… | βœ… |
| R package checks | βœ… | βœ… | βœ… |
| Quarto extension checks | βœ… | βœ… | βœ… |
| Git setup checks | βœ… | βœ… | βœ… |
| Config validation | βœ… | βœ… | βœ… |
| Hook status checks | βœ… | βœ… | βœ… |
| Cache health checks | βœ… | βœ… | βœ… |
| Scholar integration | βž• | βœ… | βœ… |
| Interactive prompts | βœ… | βœ… | βœ… |
| Install execution | βœ… | βœ… | βœ… |
| JSON CI/CD output | βœ… | βœ… | βœ… |
| Feature | Specified | Implemented | Tested |
| ----------------------- | --------- | ----------- | ------ |
| Basic health check | βœ… | βœ… | βœ… |
| --quiet flag | βœ… | βœ… | βœ… |
| --fix flag | βœ… | βœ… | βœ… |
| --json flag | βœ… | βœ… | βœ… |
| --help flag | βœ… | βœ… | βœ… |
| Dependency checks | βœ… | βœ… | βœ… |
| R package checks | βœ… | βœ… | βœ… |
| Quarto extension checks | βœ… | βœ… | βœ… |
| Git setup checks | βœ… | βœ… | βœ… |
| Config validation | βœ… | βœ… | βœ… |
| Hook status checks | βœ… | βœ… | βœ… |
| Cache health checks | βœ… | βœ… | βœ… |
| Scholar integration | βž• | βœ… | βœ… |
| Interactive prompts | βœ… | βœ… | βœ… |
| Install execution | βœ… | βœ… | βœ… |
| JSON CI/CD output | βœ… | βœ… | βœ… |

**Legend:** βœ… Required | βž• Bonus

Expand Down Expand Up @@ -187,6 +193,7 @@ Cache Health:
Summary: 28 passed, 0 warnings, 0 failures
────────────────────────────────────────────────────────────
```

</details>

### 2. Interactive Fix Mode
Expand All @@ -196,6 +203,7 @@ $ teach doctor --fix
```

**User Experience:**

- Detects missing dependencies
- Prompts: "Install X? [Y/n]"
- Executes install command
Expand Down Expand Up @@ -226,6 +234,7 @@ $ teach doctor --json
```

**GitHub Actions Example:**

```yaml
- run: teach doctor --json | jq -e '.summary.status == "healthy"'
```
Expand Down Expand Up @@ -268,12 +277,12 @@ All tests passed! βœ“

## Performance Metrics

| Metric | Target | Actual | Status |
|--------|--------|--------|--------|
| Execution Time | <5s | 2-5s | βœ… |
| Test Coverage | >80% | 100% | βœ… |
| Test Pass Rate | 100% | 100% | βœ… |
| Code Quality | A-grade | A-grade | βœ… |
| Metric | Target | Actual | Status |
| -------------- | ------- | ------- | ------ |
| Execution Time | <5s | 2-5s | βœ… |
| Test Coverage | >80% | 100% | βœ… |
| Test Pass Rate | 100% | 100% | βœ… |
| Code Quality | A-grade | A-grade | βœ… |

---

Expand All @@ -291,6 +300,7 @@ doctor)
```

**Auto-loading:**

```zsh
if [[ -z "$_FLOW_TEACH_DOCTOR_LOADED" ]]; then
local doctor_path="${0:A:h}/teach-doctor-impl.zsh"
Expand All @@ -308,6 +318,7 @@ Automatically loads teach dispatcher which loads teach-doctor-impl.zsh
### 3. CI/CD Workflows

**Example GitHub Action:**

```yaml
name: Teaching Environment Health Check
on: [push, pull_request]
Expand Down Expand Up @@ -365,6 +376,7 @@ TOTAL 6 2,165 1,880 125 160
```

**Breakdown:**

- Implementation: 620 lines
- Tests: 585 lines
- Demo: 60 lines
Expand All @@ -378,7 +390,7 @@ TOTAL 6 2,165 1,880 125 160

- βœ… Follows flow-cli conventions
- βœ… Uses standard color scheme
- βœ… Consistent function naming (_teach_doctor_*)
- βœ… Consistent function naming (_teach_doctor_\*)
- βœ… Proper error handling
- βœ… Clean separation of concerns
- βœ… No external dependencies (pure ZSH)
Expand Down Expand Up @@ -468,6 +480,7 @@ teach doctor --json | jq '.summary'
**Documentation:** Complete

**Ready for:**

- βœ… Code review
- βœ… PR to dev branch
- βœ… Release in v4.6.0
Expand All @@ -477,6 +490,7 @@ teach doctor --json | jq '.summary'
## Next Actions

1. **Commit changes:**

```bash
git add lib/dispatchers/teach-doctor-impl.zsh
git add tests/test-teach-doctor-unit.zsh
Expand All @@ -494,6 +508,7 @@ teach doctor --json | jq '.summary'
```

2. **Run final verification:**

```bash
./tests/test-teach-doctor-unit.zsh
teach doctor --help
Expand Down
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