@open-agent-toolkit/cli 0.0.10

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Files changed (797) hide show
  1. package/README.md +50 -0
  2. package/assets/agents/oat-codebase-mapper.md +275 -0
  3. package/assets/agents/oat-reviewer.md +350 -0
  4. package/assets/agents/skeptical-evaluator.md +126 -0
  5. package/assets/docs/contributing/code.md +95 -0
  6. package/assets/docs/contributing/commit-conventions.md +41 -0
  7. package/assets/docs/contributing/design-principles.md +124 -0
  8. package/assets/docs/contributing/documentation.md +69 -0
  9. package/assets/docs/contributing/hooks-and-safety.md +31 -0
  10. package/assets/docs/contributing/index.md +18 -0
  11. package/assets/docs/contributing/markdown-features.md +117 -0
  12. package/assets/docs/contributing/skills.md +68 -0
  13. package/assets/docs/guide/cli-reference.md +211 -0
  14. package/assets/docs/guide/concepts.md +88 -0
  15. package/assets/docs/guide/configuration.md +130 -0
  16. package/assets/docs/guide/documentation/commands.md +157 -0
  17. package/assets/docs/guide/documentation/index.md +27 -0
  18. package/assets/docs/guide/documentation/quickstart.md +164 -0
  19. package/assets/docs/guide/documentation/workflows.md +67 -0
  20. package/assets/docs/guide/getting-started.md +63 -0
  21. package/assets/docs/guide/ideas/index.md +34 -0
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  24. package/assets/docs/guide/provider-sync/commands.md +100 -0
  25. package/assets/docs/guide/provider-sync/config.md +77 -0
  26. package/assets/docs/guide/provider-sync/index.md +65 -0
  27. package/assets/docs/guide/provider-sync/manifest-and-drift.md +55 -0
  28. package/assets/docs/guide/provider-sync/providers.md +67 -0
  29. package/assets/docs/guide/provider-sync/scope-and-surface.md +64 -0
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  129. package/assets/skills/oat-project-subagent-implement/examples/pattern-hill-checkpoint.md +110 -0
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  134. package/assets/skills/oat-project-subagent-implement/tests/fixtures/sample-plan.md +234 -0
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@@ -0,0 +1,135 @@
1
+ #!/usr/bin/env bash
2
+ # resolve-providers.sh — Resolve active providers for instruction file analysis
3
+ #
4
+ # Usage:
5
+ # resolve-providers.sh [--providers claude,cursor,...] [--non-interactive]
6
+ #
7
+ # Resolution hierarchy:
8
+ # 1. Explicit --providers argument (comma-separated)
9
+ # 2. .oat/sync/config.json → providers.{name}.enabled
10
+ # 3. Auto-detection fallback (scan for provider directories)
11
+ # 4. Interactive confirmation (if TTY and not --non-interactive)
12
+ #
13
+ # Output: newline-separated list of provider names (always includes agents_md)
14
+ #
15
+ # Provider mapping:
16
+ # agents_md → always included (AGENTS.md is canonical)
17
+ # claude → CLAUDE.md + .claude/rules/*.md
18
+ # cursor → .cursor/rules/*.mdc, .cursor/rules/*.md
19
+ # copilot → .github/copilot-instructions.md, .github/instructions/*.instructions.md
20
+ # cline → .cline/rules/*
21
+ # codex → reads AGENTS.md natively (no additional files)
22
+
23
+ set -euo pipefail
24
+
25
+ REPO_ROOT="$(git rev-parse --show-toplevel 2>/dev/null || pwd)"
26
+ SYNC_CONFIG="${REPO_ROOT}/.oat/sync/config.json"
27
+
28
+ EXPLICIT_PROVIDERS=""
29
+ NON_INTERACTIVE=false
30
+
31
+ # Parse arguments
32
+ while [[ $# -gt 0 ]]; do
33
+ case "$1" in
34
+ --providers)
35
+ EXPLICIT_PROVIDERS="$2"
36
+ shift 2
37
+ ;;
38
+ --non-interactive)
39
+ NON_INTERACTIVE=true
40
+ shift
41
+ ;;
42
+ *)
43
+ echo "Unknown argument: $1" >&2
44
+ exit 1
45
+ ;;
46
+ esac
47
+ done
48
+
49
+ # Always start with agents_md
50
+ providers=("agents_md")
51
+
52
+ resolve_from_explicit() {
53
+ IFS=',' read -ra items <<< "$EXPLICIT_PROVIDERS"
54
+ for item in "${items[@]}"; do
55
+ item="$(echo "$item" | tr -d '[:space:]')"
56
+ if [[ -n "$item" && "$item" != "agents_md" ]]; then
57
+ providers+=("$item")
58
+ fi
59
+ done
60
+ }
61
+
62
+ resolve_from_sync_config() {
63
+ if [[ ! -f "$SYNC_CONFIG" ]] || ! jq empty "$SYNC_CONFIG" 2>/dev/null; then
64
+ return 1
65
+ fi
66
+
67
+ local found=false
68
+ for provider in claude cursor copilot cline codex; do
69
+ local enabled
70
+ enabled=$(jq -r --arg p "$provider" '.providers[$p].enabled // false' "$SYNC_CONFIG" 2>/dev/null)
71
+ if [[ "$enabled" == "true" ]]; then
72
+ providers+=("$provider")
73
+ found=true
74
+ fi
75
+ done
76
+
77
+ $found
78
+ }
79
+
80
+ resolve_from_auto_detect() {
81
+ # Scan for provider directories
82
+ [[ -d "${REPO_ROOT}/.claude" || -f "${REPO_ROOT}/CLAUDE.md" ]] && providers+=("claude")
83
+ [[ -d "${REPO_ROOT}/.cursor" ]] && providers+=("cursor")
84
+ [[ -d "${REPO_ROOT}/.github/instructions" || -f "${REPO_ROOT}/.github/copilot-instructions.md" ]] && providers+=("copilot")
85
+ [[ -d "${REPO_ROOT}/.cline" ]] && providers+=("cline")
86
+ }
87
+
88
+ interactive_confirm() {
89
+ if $NON_INTERACTIVE || [[ ! -t 0 ]]; then
90
+ return
91
+ fi
92
+
93
+ # Show detected providers and ask about additional ones
94
+ local detected
95
+ detected=$(printf '%s\n' "${providers[@]}" | sort -u | grep -v '^agents_md$' || true)
96
+
97
+ if [[ -n "$detected" ]]; then
98
+ echo "Detected providers: agents_md $(echo "$detected" | tr '\n' ' ')" >&2
99
+ else
100
+ echo "Detected providers: agents_md (no provider-specific formats found)" >&2
101
+ fi
102
+
103
+ echo "" >&2
104
+ echo "Available providers: claude, cursor, copilot, cline, codex" >&2
105
+ echo -n "Add any additional providers? (comma-separated, or Enter to skip): " >&2
106
+ read -r additional
107
+
108
+ if [[ -n "$additional" ]]; then
109
+ IFS=',' read -ra items <<< "$additional"
110
+ for item in "${items[@]}"; do
111
+ item="$(echo "$item" | tr -d '[:space:]')"
112
+ if [[ -n "$item" && "$item" != "agents_md" ]]; then
113
+ providers+=("$item")
114
+ fi
115
+ done
116
+ fi
117
+ }
118
+
119
+ # Resolution hierarchy
120
+ if [[ -n "$EXPLICIT_PROVIDERS" ]]; then
121
+ # 1. Explicit argument overrides everything
122
+ resolve_from_explicit
123
+ elif resolve_from_sync_config; then
124
+ # 2. Sync config found and had providers
125
+ :
126
+ else
127
+ # 3. Auto-detection fallback
128
+ resolve_from_auto_detect
129
+ fi
130
+
131
+ # 4. Interactive confirmation (unless --non-interactive)
132
+ interactive_confirm
133
+
134
+ # Deduplicate and output
135
+ printf '%s\n' "${providers[@]}" | sort -u
@@ -0,0 +1,507 @@
1
+ ---
2
+ name: oat-agent-instructions-apply
3
+ version: 1.6.1
4
+ description: Run when you have an agent instructions analysis artifact and want to generate or update instruction files. Creates a branch, generates files from templates, and optionally opens a PR.
5
+ disable-model-invocation: true
6
+ user-invocable: true
7
+ allowed-tools: Read, Write, Edit, Bash(git:*), Bash(gh:*), Glob, Grep, AskUserQuestion
8
+ ---
9
+
10
+ # Agent Instructions Apply
11
+
12
+ Generate or update agent instruction files based on an analysis artifact, with user review and PR-based workflow.
13
+
14
+ ## Prerequisites
15
+
16
+ - Git repository with a recent analysis artifact in `.oat/repo/analysis/`.
17
+ - If no analysis exists, run `oat-agent-instructions-analyze` first.
18
+ - `jq` available in PATH (used by helper scripts).
19
+ - `gh` CLI available for PR creation (optional — manual fallback provided).
20
+
21
+ ## Mode Assertion
22
+
23
+ **OAT MODE: Agent Instructions Apply**
24
+
25
+ **Purpose:** Generate and update instruction files based on analysis findings, with user approval at each step.
26
+
27
+ **BLOCKED Activities:**
28
+
29
+ - No generating files the user hasn't approved.
30
+ - No pushing to remote without user confirmation.
31
+ - No modifying files outside the instruction file scope.
32
+
33
+ **ALLOWED Activities:**
34
+
35
+ - Reading analysis artifacts, instruction files, and project configuration.
36
+ - Running helper scripts for provider resolution and tracking.
37
+ - Creating/updating instruction files per approved plan.
38
+ - Creating branches, committing, and pushing (with user confirmation).
39
+ - Writing tracking updates to `.oat/tracking.json`.
40
+
41
+ ## Question Handling Across Hosts
42
+
43
+ When this skill needs a user decision:
44
+
45
+ 1. Use `AskUserQuestion` when running in Claude Code with tool availability.
46
+ 2. Use Codex structured user-input tooling when available in the current Codex host/runtime.
47
+ 3. Otherwise ask the same question in plain conversational text.
48
+
49
+ Keep the question content consistent across hosts so the workflow remains portable even when the UI differs.
50
+
51
+ ## Analyze vs Apply Boundary
52
+
53
+ Treat the analysis output as the source of truth for what should be generated and why.
54
+
55
+ When a companion bundle exists beside the markdown artifact, the bundle is the primary generation contract:
56
+
57
+ - `agent-instructions-<timestamp>.bundle/recommendations.yaml`
58
+ - `agent-instructions-<timestamp>.bundle/packs/*.md`
59
+
60
+ The markdown artifact remains the human-readable review summary.
61
+
62
+ Apply may:
63
+
64
+ - read the exact evidence sources cited by the artifact
65
+ - verify that cited files still exist
66
+ - translate approved recommendations into concrete instruction text
67
+
68
+ Apply must **not**:
69
+
70
+ - invent unsupported conventions
71
+ - infer formatting/style rules from defaults or a small sample
72
+ - create new recommendations that are not present in the artifact
73
+ - silently fill in missing evidence gaps
74
+
75
+ ## Progress Indicators (User-Facing)
76
+
77
+ - Print a phase banner once at start:
78
+
79
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
80
+ OAT ▸ AGENT INSTRUCTIONS APPLY
81
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
82
+
83
+ - Step indicators:
84
+ - `[1/7] Loading analysis artifact…`
85
+ - `[2/7] Building recommendation plan…`
86
+ - `[3/7] Reviewing plan with user…`
87
+ - `[4/7] Creating branch…`
88
+ - `[5/7] Generating instruction files…`
89
+ - `[6/7] Committing + PR…`
90
+ - `[7/7] Updating tracking + summary…`
91
+
92
+ ## Process
93
+
94
+ ### Step 0: Intake — Find Analysis Artifact
95
+
96
+ Search for the most recent analysis artifact:
97
+
98
+ ```bash
99
+ ls -t .oat/repo/analysis/agent-instructions-*.md 2>/dev/null | head -1
100
+ ```
101
+
102
+ If found, derive the companion bundle path:
103
+
104
+ ```bash
105
+ BUNDLE_DIR="${ARTIFACT_PATH%.md}.bundle"
106
+ MANIFEST_PATH="${BUNDLE_DIR}/recommendations.yaml"
107
+ ```
108
+
109
+ **If found:** Read the artifact, then check for the companion bundle.
110
+
111
+ **Bundle-first behavior:**
112
+
113
+ - If `"$BUNDLE_DIR"` exists, validate `summary.md`, `recommendations.yaml`, and every referenced pack file.
114
+ - Treat the bundle as the primary generation contract and the markdown artifact as review context.
115
+ - If the bundle exists but is incomplete, stop and require a refreshed analysis rather than falling back silently to the
116
+ markdown artifact.
117
+
118
+ **Legacy fallback:**
119
+
120
+ - If no companion bundle exists, continue using the markdown artifact alone.
121
+ - This keeps apply backward compatible with older analysis artifacts until the bundle contract is fully adopted.
122
+
123
+ Validate that the artifact includes evidence, confidence, and progressive disclosure decisions for each recommendation.
124
+ Also validate that every `link_only` recommendation includes at least one concrete link target to a canonical doc, config, or example.
125
+ If a recommendation updates or contradicts an existing rule, validate that it also includes `Content Guidance`,
126
+ `Must Include`, `Must Not Include`, `Preferred Default for New Files`, and `Claim Corrections`.
127
+ If the artifact records a High/Medium glob-scoped opportunity with a recommended action to create, update, or split a
128
+ rule, validate that a matching explicit recommendation exists. Apply should not infer missing rule work from the
129
+ opportunities table.
130
+ If the companion bundle exists, validate that:
131
+
132
+ - every recommendation has a stable ID
133
+ - every manifest entry points to an existing pack file
134
+ - each pack preserves the executable fields apply relies on (`Evidence`, `Content Guidance`, `Must Include`,
135
+ `Must Not Include`, `Counter-Examples`, `New-File Workflow`, `Preferred Default for New Files`, `Claim Corrections`)
136
+
137
+ If the artifact is missing that detail, treat it as incomplete:
138
+
139
+ ```
140
+ Analysis artifact is missing evidence-backed recommendation detail.
141
+ Re-run oat-agent-instructions-analyze before applying changes.
142
+ ```
143
+
144
+ Then stop.
145
+
146
+ **If not found:** Tell the user:
147
+
148
+ ```
149
+ No analysis artifact found in .oat/repo/analysis/.
150
+ Run oat-agent-instructions-analyze first to scan the codebase.
151
+ ```
152
+
153
+ Then stop.
154
+
155
+ ### Step 1: Resolve Providers
156
+
157
+ ```bash
158
+ SCRIPT_DIR=".agents/skills/oat-agent-instructions-analyze/scripts"
159
+ TRACKING_SCRIPT=".oat/scripts/resolve-tracking.sh"
160
+ PROVIDERS=$(bash "$SCRIPT_DIR/resolve-providers.sh" --non-interactive)
161
+ ```
162
+
163
+ The provider list determines which file formats to generate. If running interactively, omit `--non-interactive` to allow the user to confirm or add providers.
164
+
165
+ ### Step 2: Build Recommendation Plan
166
+
167
+ For each recommendation in the analysis artifact, determine the action.
168
+ Recommendations may originate from findings, provider baseline gaps, directory coverage gaps, or promoted glob-rule opportunities.
169
+ The artifact should already specify the rationale, evidence, confidence, and disclosure decision.
170
+ Do not rediscover conventions from scratch during this step.
171
+ When the companion bundle exists, build the plan from the bundle manifest and recommendation packs first, then use the
172
+ markdown artifact only to confirm reviewer-facing rationale and summary wording.
173
+ Carry forward the artifact's structured handoff fields (`Content Guidance`, `Must Include`, `Must Not Include`,
174
+ `Counter-Examples`, `New-File Workflow`, `Preferred Default for New Files`, `Claim Corrections`) into the plan wherever
175
+ they are present.
176
+ When the companion bundle exists, also carry forward the stable `Recommendation ID` and `Bundle Pack` path for each
177
+ recommendation so plan review and generation stay aligned to the same pack file.
178
+
179
+ **For provider baseline gaps (always-on provider files):**
180
+
181
+ - Treat them as first-class recommendations from the artifact, not as implied apply-time behavior
182
+ - Examples include missing Claude `CLAUDE.md` import shims and missing `.github/copilot-instructions.md` shims
183
+ - Carry forward the artifact's evidence refs, confidence, and disclosure mode into the plan
184
+ - If the artifact marks a provider-baseline recommendation `omit`, do not include it in the apply plan
185
+ - If the artifact marks a provider-baseline recommendation `ask_user`, include it with the evidence and require explicit user approval
186
+
187
+ **For coverage gaps (new files):**
188
+
189
+ - Determine the target file path based on the directory and provider
190
+ - Select the appropriate template from `references/instruction-file-templates/`
191
+ - For AGENTS.md files: use `agents-md-root.md` or `agents-md-scoped.md`
192
+ - For glob-scoped rules: use `glob-scoped-rule.md` as the canonical body and write a canonical rule file to `.agents/rules/{name}.md`
193
+ - Carry forward the artifact's evidence refs, confidence, and disclosure mode into the plan
194
+ - If the artifact marks a coverage-gap recommendation `omit`, do not include it in the apply plan
195
+ - If the artifact marks a coverage-gap recommendation `ask_user`, include it with the evidence and require explicit user approval
196
+ - If a `link_only` coverage-gap recommendation has no link target, stop and ask for a fresh analysis instead of guessing
197
+
198
+ **For quality findings (updates to existing files):**
199
+
200
+ - Identify the specific issue and the fix
201
+ - Preserve existing manual customizations — only modify the problematic section
202
+ - If the artifact marks a recommendation `omit`, do not include it in the apply plan
203
+ - If the artifact marks a recommendation `ask_user`, include it with the evidence and require explicit user approval
204
+ - If the change corrects an existing rule claim, treat the artifact's `Claim Corrections` and `Must Not Include`
205
+ fields as mandatory constraints rather than optional hints
206
+ - If evidence is missing or stale, stop and ask for a fresh analysis instead of guessing
207
+
208
+ **For competing sub-patterns in glob-scoped rules:**
209
+
210
+ - Treat the artifact's recommendation as authoritative about which pattern new files should follow
211
+ - If both patterns remain valid, document both and explicitly call out the recommended default for new files
212
+ - If the artifact reports a split but does not identify the preferred direction for new files, stop and ask for a
213
+ refreshed analysis instead of guessing
214
+
215
+ **Multi-format composition order:**
216
+
217
+ 1. **AGENTS.md first** — the canonical, provider-agnostic file
218
+ 2. **CLAUDE.md** — if claude provider is active, ensure `@AGENTS.md` import exists
219
+ 3. **Glob-scoped rules** — author once in canonical format at `.agents/rules/{name}.md` with YAML frontmatter (`description`, `globs`, `activation`)
220
+ - Provider-specific rule files are generated by `oat sync --scope project`
221
+ - Do not hand-author `.claude/rules/*.md`, `.cursor/rules/*.mdc`, or `.github/instructions/*.instructions.md`
222
+ 4. **Copilot shim** — if copilot provider is active, generate `.github/copilot-instructions.md` from `frontmatter/copilot-shim.md` template
223
+
224
+ Fill the apply plan template at `references/apply-plan-template.md` with each recommendation.
225
+
226
+ Persist the exact markdown plan shown to the user as `APPLY_PLAN_MARKDOWN` (including recommendation tables and the summary table). This is the source that must be embedded in the PR description.
227
+
228
+ ### Step 3: User Reviews Plan
229
+
230
+ Present the full recommendation plan to the user first, then ask which review mode they want:
231
+
232
+ - **apply all** — approve the full set as presented
233
+ - **apply interactively** — switch to recommendation-by-recommendation review
234
+ - **discuss** — pause for questions, adjustments, or scope changes before approval
235
+ - **cancel** — stop without applying anything
236
+
237
+ For the review-mode choice:
238
+
239
+ - Claude Code: use `AskUserQuestion`
240
+ - Codex: use structured user-input tooling when available in the current host/runtime
241
+ - Fallback: ask in plain text
242
+
243
+ The prompt should ask for exactly one of: `apply all`, `apply interactively`, `discuss`, `cancel`.
244
+
245
+ If the user chooses **cancel**, output "No actions approved. Exiting." and stop.
246
+
247
+ If the user chooses **apply all**:
248
+
249
+ - confirm that the full plan is approved
250
+ - capture any global notes that apply across the whole plan
251
+ - treat all non-blocked recommendations as approved unless the user names exceptions
252
+
253
+ If the user chooses **apply interactively**:
254
+
255
+ - for each recommendation, ask:
256
+ - **approve** — proceed with generation
257
+ - **modify** — approve with user-specified changes
258
+ - **skip** — do not act on this recommendation
259
+ - use the same host-specific question handling (`AskUserQuestion` / Codex structured input when available / plain text fallback)
260
+ - wait for user decisions on all recommendations before proceeding
261
+
262
+ If the user chooses **discuss**:
263
+
264
+ - answer questions and revise the plan if needed
265
+ - re-present the updated plan and ask again: `apply all`, `apply interactively`, `discuss`, or `cancel`
266
+
267
+ If all recommendations are skipped, output "No actions approved. Exiting." and stop.
268
+
269
+ Build an `APPLIED_PLAN_DETAILS` block from approved/modified recommendations with:
270
+
271
+ - Recommendation ID
272
+ - Action (create/update)
273
+ - Target path
274
+ - Provider
275
+ - Disclosure
276
+ - Evidence refs
277
+ - Decision (`approved_via_apply_all` / `approved` / `modified`)
278
+ - User notes (if any)
279
+
280
+ Also build `APPLIED_PLAN_MARKDOWN`: a markdown block containing only the approved/modified recommendation sections from the presented plan, preserving table formatting.
281
+
282
+ ### Step 4: Create Branch
283
+
284
+ ```bash
285
+ TIMESTAMP=$(date -u +"%Y-%m-%d-%H%M")
286
+ BRANCH="oat/agent-instructions-${TIMESTAMP}"
287
+ git checkout -b "$BRANCH"
288
+ ```
289
+
290
+ If branch creation fails (e.g., uncommitted changes), ask the user to resolve and retry.
291
+
292
+ ### Step 5: Generate/Update Instruction Files
293
+
294
+ For each approved recommendation, in the order from Step 2:
295
+
296
+ - When the companion bundle exists, load the approved recommendation's manifest entry and matching pack before
297
+ reading repo evidence or generating content.
298
+ - Treat that pack as the executable contract for the recommendation. Do not generate from the markdown summary alone.
299
+
300
+ **Creating new files:**
301
+
302
+ 1. Read the appropriate template from `references/instruction-file-templates/`.
303
+ 2. Read only the project context needed to fill the approved recommendation:
304
+ - the matching recommendation pack when the companion bundle exists
305
+ - the evidence files cited in the artifact
306
+ - `package.json` for commands and dependencies
307
+ - directory structure for architecture section
308
+ - existing instruction files for consistency
309
+ 3. Generate the file content by filling the template with project-specific details from the cited evidence.
310
+ 4. Preserve progressive disclosure decisions from the artifact:
311
+ - `inline` → keep the essential rule in the instruction file
312
+ - `link_only` → add a concise pointer to the canonical doc/config/example
313
+ - `omit` → do not encode the item in the instruction file
314
+ - `ask_user` → require explicit user confirmation before writing
315
+ 5. Follow the recommendation's structured handoff fields during generation:
316
+ - `Content Guidance` shapes emphasis and phrasing
317
+ - `Must Include` is mandatory content
318
+ - `Must Not Include` is prohibited content
319
+ - `Preferred Default for New Files` determines which sub-pattern new files should follow
320
+ - `Claim Corrections` replaces stale claims in updated files
321
+ 6. For glob-scoped rules:
322
+ - Write the canonical markdown once to `.agents/rules/{name}.md`
323
+ - Include canonical rule frontmatter (`description`, `globs`, `activation`) instead of provider-specific wrappers
324
+ - After writing canonical rules, run `oat sync --scope project` to generate provider-specific rule files
325
+ - Verify the generated provider files exist for each active provider instead of maintaining them by hand
326
+ - Verify each generated provider file is trackable with `git check-ignore`; if any generated file is ignored,
327
+ stop and surface the exact paths before committing
328
+
329
+ **Updating existing files:**
330
+
331
+ 1. Read the existing file and the matching recommendation pack when the companion bundle exists.
332
+ 2. Identify the section(s) that need updating based on the finding.
333
+ 3. Make targeted edits using only the approved recommendation and its cited evidence.
334
+ 4. Do not rewrite the entire file unless the user explicitly approves.
335
+
336
+ **Negative rules:**
337
+
338
+ - Do not add tabs-vs-spaces, quote style, import sorting, naming, or similar formatting rules unless the artifact cites repo evidence for them.
339
+ - Do not upgrade a repeated code pattern into a hard instruction unless the artifact already approved it.
340
+ - If formatter/linter config exists, prefer `run formatter/lint` or a link to the config/doc over prose restatement of the same rule.
341
+ - Do not soften specific runtime versions, infrastructure notes, commit conventions, or rule corrections into vague prose
342
+ when the artifact or cited evidence is explicit.
343
+ - If a cited source no longer exists, stop that recommendation and ask for a fresh analysis or user guidance.
344
+
345
+ **Required context — read these bundled skill docs before generating:**
346
+
347
+ These docs are bundled with this skill under `references/docs/` and should be read from that location,
348
+ not from repo-root `.agents/docs/`.
349
+
350
+ - `references/docs/agent-instruction.md` — quality criteria and best practices
351
+ - `references/docs/rules-files.md` — cross-provider format reference
352
+ - `references/docs/cursor-rules-files.md` — Cursor-specific `.mdc` format (if cursor provider is active)
353
+
354
+ ### Step 6: Commit and PR
355
+
356
+ **Stage and commit:**
357
+
358
+ ```bash
359
+ git add {list of generated/updated files}
360
+ git commit -m "chore: update agent instruction files
361
+
362
+ Generated by oat-agent-instructions-apply from analysis artifact.
363
+ Files: {count} created, {count} updated."
364
+ ```
365
+
366
+ **Offer to open a PR:**
367
+
368
+ After committing, proactively ask the user if they'd like to open a pull request. Frame this as the recommended next step:
369
+
370
+ ```
371
+ Changes committed. Would you like me to push and open a pull request?
372
+ The PR will include the applied plan summary and the full analysis artifact for reference.
373
+ ```
374
+
375
+ Use host-specific question handling:
376
+
377
+ - Claude Code: use `AskUserQuestion`
378
+ - Codex: use structured user-input tooling when available in the current host/runtime
379
+ - Fallback: ask in plain text
380
+
381
+ **If creating PR:**
382
+
383
+ The PR body must include:
384
+
385
+ 1. **Overview** — why this PR exists, source analysis artifact, and provider scope.
386
+ 2. **Applied Plan Details** — the exact plan markdown presented in terminal (tables included), filtered to approved/modified recommendations.
387
+ 3. **Full Analysis Artifact** — the complete analysis in a collapsible `<details>` section at the bottom so reviewers can see the evidence behind every change.
388
+
389
+ ```bash
390
+ git push -u origin "$(git rev-parse --abbrev-ref HEAD)"
391
+ gh pr create --base main \
392
+ --title "chore: update agent instruction files" \
393
+ --body "$(cat <<'PRBODY'
394
+ ## Overview
395
+
396
+ - Generated/updated agent instruction files based on analysis
397
+ - Source: {analysis-artifact-path}
398
+ - Providers: {provider-list}
399
+ - Result: {N} created, {N} updated, {N} skipped
400
+
401
+ ## Applied Plan Details
402
+
403
+ The following section is copied from the presented apply plan (`APPLY_PLAN_MARKDOWN`), preserving its tables:
404
+
405
+ {APPLY_PLAN_MARKDOWN}
406
+
407
+ ## Applied Plan Summary
408
+
409
+ | Rec # | Action | Target | Provider | Decision | Notes |
410
+ |------:|--------|--------|----------|----------|-------|
411
+ | {1} | {create/update} | `{path}` | {provider} | {approved/modified} | {note or "-"} |
412
+ | ... | ... | ... | ... | ... | ... |
413
+
414
+ ## Changes
415
+
416
+ {list of files created/updated with brief rationale}
417
+
418
+ ## Verification
419
+
420
+ - [ ] Instruction files follow quality checklist
421
+ - [ ] No content duplication across formats
422
+ - [ ] Glob-scoped rules have identical body content across providers
423
+ - [ ] Commands referenced in instruction files are valid
424
+ - [ ] Every non-obvious convention in generated text is backed by cited analysis evidence
425
+
426
+ ---
427
+
428
+ ## Full Analysis Artifact
429
+
430
+ The complete analysis that produced these recommendations is included below for reviewer reference.
431
+
432
+ <details>
433
+ <summary>Click to expand full analysis</summary>
434
+
435
+ {full contents of the analysis artifact markdown file}
436
+
437
+ </details>
438
+ PRBODY
439
+ )"
440
+ ```
441
+
442
+ **If the user declines PR creation:**
443
+
444
+ ```
445
+ Options:
446
+ 1. Push only (create PR manually)
447
+ 2. Keep local (no push)
448
+ ```
449
+
450
+ **If `gh` is not available or fails:**
451
+
452
+ ```
453
+ PR creation failed. To create manually:
454
+ 1. Push: git push -u origin {branch}
455
+ 2. Open PR at your repository's web interface
456
+ 3. Use the structure above in the PR body, including the full analysis in a collapsible section at the bottom
457
+ ```
458
+
459
+ ### Step 7: Update Tracking and Output Summary
460
+
461
+ **Update tracking:**
462
+
463
+ ```bash
464
+ TRACKING_SCRIPT=".oat/scripts/resolve-tracking.sh"
465
+ ROOT_TARGET=$(bash "$TRACKING_SCRIPT" root)
466
+ ROOT_HASH=$(echo "$ROOT_TARGET" | jq -r '.commitHash')
467
+ ROOT_BRANCH=$(echo "$ROOT_TARGET" | jq -r '.baseBranch')
468
+
469
+ bash "$TRACKING_SCRIPT" write \
470
+ agentInstructionsApply \
471
+ "$ROOT_HASH" \
472
+ "$ROOT_BRANCH" \
473
+ "apply" \
474
+ {providers...}
475
+ ```
476
+
477
+ **Output summary:**
478
+
479
+ ```
480
+ Apply complete.
481
+
482
+ Files created: {N}
483
+ Files updated: {N}
484
+ Files skipped: {N}
485
+ Providers: {list}
486
+ Branch: {branch-name}
487
+ PR: {URL or "not created"}
488
+
489
+ Source analysis: {artifact-path}
490
+ Tracking updated: .oat/tracking.json
491
+ ```
492
+
493
+ ## Deferred from v1
494
+
495
+ - `AGENTS.override.md` generation and management
496
+ - Auto-apply mode (skip user review for low-severity recommendations)
497
+ - Batch update across multiple repos
498
+
499
+ ## References
500
+
501
+ - Bundled quality criteria: `references/docs/agent-instruction.md`
502
+ - Bundled cross-provider rules reference: `references/docs/rules-files.md`
503
+ - Bundled Cursor-specific format reference: `references/docs/cursor-rules-files.md`
504
+ - Analysis artifact: `.oat/repo/analysis/agent-instructions-*.md`
505
+ - Templates: `references/instruction-file-templates/`
506
+ - Apply plan template: `references/apply-plan-template.md`
507
+ - Tracking script: `.oat/scripts/resolve-tracking.sh`