chore: refresh agent-skills propose — skills/ at project root, delete docs/skills/

Rewrites the propose doc (revision 5) to use skills/ at project root
instead of agent-skills/ + compile pipeline. All hosts read from skills/
directly. No compile step.

- Move propose to propose/active/ per new folder structure
- Delete docs/skills/ (java-codebase-explore.md, .zip) and
  scripts/build-explore-skill.sh
- Add hints_structured awareness (principle #10, decision #17)
- Collapse 5-PR → 4-PR migration (no compile step PR)
- Update README, AGENTS.md, test.yml, tests/README, automation README

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: HumanBean17

.github/workflows/test.yml

@@ -23,7 +23,7 @@ jobs:
               - 'docs/**'
               - 'propose/**'
               - 'plans/**'
-              - 'reports/**'
+              - 'skills/**'
               - '.agents/**'
               - 'AGENTS.md'
               - 'README.md'

AGENTS.md

@@ -42,6 +42,7 @@ when needed.
 - `docs/CODEBASE_REQUIREMENTS.md` — Java-repo assumptions and per-file map of
   what to edit when a target tree doesn't match defaults.
 - `tests/README.md` — testing philosophy.
+- **`skills/`** — user-facing skills shipped to java-codebase-rag consumers (navigation, workflow). Developer workflow skills live in **`.agents/skills/`**, not here.
 - **`propose/`** — design proposes. **In-flight** proposes live in
   **`propose/active/`**. **`propose/completed/`** — landed work and rationale.
   **List or search this tree** for current filenames; do not rely on enumerated

README.md

@@ -98,7 +98,7 @@ See [`mcp.json.example`](./mcp.json.example) for the same shape in `.mcp.json` (
 ### Driving the MCP from an agent
 
 - **[`docs/AGENT-GUIDE.md`](./docs/AGENT-GUIDE.md)** — standalone MCP operating manual (copy-paste into `QWEN.md` / `CLAUDE.md` / `AGENTS.md`): five tools, `NodeFilter`, edge taxonomy, required `neighbors` arguments, ontology glossary, recovery playbook, slash-style aliases.
-- **[`docs/skills/java-codebase-explore.md`](./docs/skills/java-codebase-explore.md)** — exploration **strategy** (missions, fallbacks, anti-capabilities, stopping rules); `AGENT-GUIDE.md` remains the **operating manual** for tool shapes and recovery.
+- **[`skills/`](./skills/)** — user-facing navigation and workflow skills for java-codebase-rag consumers. Skills are `SKILL.md` files; agents discover them via slash-names (`/callees`, `/routes`, etc.). See [`propose/active/AGENT-SKILLS-AND-COMMANDS-PROPOSE.md`](./propose/active/AGENT-SKILLS-AND-COMMANDS-PROPOSE.md) for the full Tier 1 + Tier 2 skill set.
 - **[`docs/MANUAL-VERIFICATION-CHECKLIST.md`](./docs/MANUAL-VERIFICATION-CHECKLIST.md)** — 7-phase agent-driven verification you run after indexing your real project.
 
 ---
@@ -156,7 +156,7 @@ Run `java-codebase-rag --help` to list grouped subcommands. Operator playbook wi
 | [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md) | Environment variables, project YAML, graph ontology, brownfield overrides, ignore patterns. |
 | [`docs/JAVA-CODEBASE-RAG-CLI.md`](./docs/JAVA-CODEBASE-RAG-CLI.md) | CLI operator playbook: workflows, exit codes, env alignment. |
 | [`docs/EDGE-NAVIGATION.md`](./docs/EDGE-NAVIGATION.md) | MCP-traversable edges, directions, dot-key composition. |
-| [`docs/skills/java-codebase-explore.md`](./docs/skills/java-codebase-explore.md) | Agent exploration skill (strategy, missions, fallbacks); packaged zip [`docs/skills/java-codebase-explore.zip`](./docs/skills/java-codebase-explore.zip) for Perplexity-style hosts. |
+| [`skills/`](./skills/) | User-facing skills for java-codebase-rag consumers. Navigation and workflow skills (Tier 1 + Tier 2) planned — see [`propose/active/AGENT-SKILLS-AND-COMMANDS-PROPOSE.md`](./propose/active/AGENT-SKILLS-AND-COMMANDS-PROPOSE.md). |
 | [`docs/MANUAL-VERIFICATION-CHECKLIST.md`](./docs/MANUAL-VERIFICATION-CHECKLIST.md) | 7-phase agent-driven verification after indexing your project. |
 | [`docs/CODEBASE_REQUIREMENTS.md`](./docs/CODEBASE_REQUIREMENTS.md) | Assumptions about your Java repo + per-file edit map for non-conforming codebases. |
 | [`automation/cursor_propose_only/README.md`](./automation/cursor_propose_only/README.md) | Optional proposal orchestration workflow (single-command autopilot, planning bundles, automated execution/review loops). |

automation/cursor_propose_only/README.md

@@ -21,7 +21,7 @@ If you only want a subset, pass `--proposal` multiple times:
 .venv/bin/python automation/cursor_propose_only/cli.py prepare \
   --repo-root . \
   --proposal-dir propose \
-  --output-dir reports/propose_automation_selected \
+  --output-dir .agents/reports/propose_automation_selected \
   --proposal HTTP-ROUTE-METHOD-ENUM-PROPOSE.md \
   --proposal ENHANCED-ROLE-RECOGNITION-PROPOSE.md \
   --rounds 3 \
@@ -40,18 +40,18 @@ Notes:
 .venv/bin/python automation/cursor_propose_only/cli.py prepare \
   --repo-root . \
   --proposal-dir propose \
-  --output-dir reports/propose_automation \
+  --output-dir .agents/reports/propose_automation \
   --rounds 3 \
   --min-severity medium
 ```
 
 Generated artifacts:
 
-- `reports/propose_automation/workflow.json`
-- `reports/propose_automation/jobs/<job-id>/planner_prompt.md`
-- `reports/propose_automation/jobs/<job-id>/reviewer_prompt_round1.md`
-- `reports/propose_automation/jobs/<job-id>/reviewer_prompt_round2.md`
-- `reports/propose_automation/jobs/<job-id>/reviewer_prompt_round3.md`
+- `.agents/reports/propose_automation/workflow.json`
+- `.agents/reports/propose_automation/jobs/<job-id>/planner_prompt.md`
+- `.agents/reports/propose_automation/jobs/<job-id>/reviewer_prompt_round1.md`
+- `.agents/reports/propose_automation/jobs/<job-id>/reviewer_prompt_round2.md`
+- `.agents/reports/propose_automation/jobs/<job-id>/reviewer_prompt_round3.md`
 
 ## Evaluate each reviewer response
 
@@ -60,7 +60,7 @@ then evaluate it with severity gating.
 
 ```bash
 .venv/bin/python automation/cursor_propose_only/cli.py evaluate \
-  --workflow reports/propose_automation/workflow.json \
+  --workflow .agents/reports/propose_automation/workflow.json \
   --job-id <job-id> \
   --round 1 \
   --review-file /path/to/review_round1.md \
@@ -83,7 +83,7 @@ tasks as `ready_to_merge` / `merged`.
 ```bash
 .venv/bin/python automation/cursor_propose_only/execute.py \
   --repo-root . \
-  --workflow reports/propose_automation/workflow.json \
+  --workflow .agents/reports/propose_automation/workflow.json \
   --rounds 3 \
   --min-severity medium \
   --implementation-command 'cursor-agent run --model auto --prompt-file {task_prompt_file}' \
@@ -97,7 +97,7 @@ Notes:
 - without `--run`, `execute.py` performs a dry-run and only stages prompts/state
 - command templates support placeholders such as `{task_prompt_file}`,
   `{review_prompt_file}`, `{pr_url}`, `{branch}`, `{base}`, `{round}`
-- workflow state is persisted in `reports/propose_automation/workflow.json`
+- workflow state is persisted in `.agents/reports/propose_automation/workflow.json`
 
 ## Fully automated (single command)
 
@@ -108,7 +108,7 @@ use `autopilot.py`.
 .venv/bin/python automation/cursor_propose_only/autopilot.py \
   --repo-root . \
   --proposal-dir propose \
-  --output-dir reports/propose_automation_selected \
+  --output-dir .agents/reports/propose_automation_selected \
   --proposal TIER2-INCREMENTAL-REBUILD-PROPOSE.md \
   --planning-rounds 2 \
   --planning-min-severity medium \