feat(obsidian): add vault status dashboard

[Aidenwu0209]

Summary

This PR fixes one issue: Obsidian-enabled vaults now get a generated status dashboard and reusable Agent workflow entrypoints.

Closes #62.

Layer

• docs
• skill
• adapter
• runtime
• schema
• safety
• eval
• ux
• human-review
• release

Severity

• P0
• P1
• P2
• P3

DeepSeek full-flow context

• Workspace: /Users/wu/Desktop/wu/AAaabaidu/LLM-Wiki
• Run ID: 20260506-143821-issue62-optimization
• Run dir: /Users/wu/Desktop/wu/AAaabaidu/LLM-Wiki /runs/20260506-143821-issue62-optimization
• Vault dir: N/A - issue #62 Obsidian workflow optimization did not require a DeepSeek full-flow vault
• Paper dir: /Users/wu/Desktop/wu/AAaabaidu/LLM-Wiki /deepseek_paper
• Repository commit before fix: 683ccbcaba68bef9e5d6ac38996206a0ba887860

Product UX evidence, if applicable

• Obsidian first-open screenshot: N/A
• Obsidian before screenshot: N/A
• Obsidian after screenshot: N/A
• Obsidian UX report: N/A
• Query/writeback transcript or report: N/A
• Was explicit writeback approval obtained: not applicable

Do not commit screenshots containing private or sensitive content unless the user explicitly approves. If screenshots are local-only evidence, include their local paths and a concise description in the PR body.

Problem

wiki_init.py --obsidian configured Obsidian settings and inbox/sort resources, but the generated vault still lacked a first-screen status dashboard, clear Agent command entrypoints, reusable prompt templates, and a Homepage target that surfaces review/writeback safety boundaries.

Minimal reproduction

uv run python scripts/wiki_init.py <new-vault> --repo-root . --obsidian --obsidian-skip-downloads
find <new-vault> -maxdepth 3 -name '_dashboard.md' -o -path '*/templates/agent-prompts/*'

Observed:

No generated dashboard or Agent prompt templates were created.
Homepage default pointed at index instead of a status dashboard.

Expected:

An Obsidian-enabled vault should expose a generated dashboard/status page, prompt templates, common runtime commands, and proposal-first writeback guidance without overwriting user-edited dashboard files.

Root cause

The optional Obsidian setup layer only handled Obsidian settings/plugins/profile resources. There was no runtime command for vault status/dashboard generation, and wiki_init.py --obsidian had no scaffold for Agent context files or prompt templates beyond the generic source/concept templates.

Fix

Added scripts/wiki_status.py to summarize vault health and optionally write _dashboard.md; wired wiki_init.py --obsidian to create _dashboard.md, AGENTS.md, CLAUDE.md, and templates/agent-prompts/; changed Homepage defaults to _dashboard; added docs, checklist, CI, quality checks, and runtime eval coverage.

Changed files:

• scripts/wiki_status.py - new dashboard/status generator with protected output boundaries.
• scripts/wiki_init.py - copies the status runtime and writes Obsidian dashboard/context files without overwriting existing dashboard unless --force.
• scripts/wiki_obsidian_setup.py - points Homepage at _dashboard and writes plugin data even when downloads are skipped.
• templates/agent-prompts/* - reusable Agent workflows for ingest, query, writeback, lint, review, concept revision, and graph export.
• scripts/check_quality.py, scripts/wiki_eval.py, .github/workflows/validate.yml - smoke tests and CI coverage.
• Docs/checklist/schema/sortspec files - document and surface the new workflow.

Before / after

Before:

Obsidian profile created settings and inbox/sort files, but users still had to infer workflow state and safe Agent actions from docs/scripts.

After:

Fresh Obsidian-enabled vaults open to `_dashboard.md`, show pipeline status/review queues/recent reports/common commands/prompt templates, and preserve proposal-first writeback and review gates.

Validation

Commands run:

python3 -m py_compile scripts/wiki_status.py scripts/wiki_init.py scripts/wiki_obsidian_setup.py scripts/check_quality.py scripts/wiki_eval.py scripts/wiki_lint.py
python3 scripts/wiki_status.py --help
python3 scripts/wiki_status.py examples/minimal-vault
python3 scripts/wiki_init.py "$RUN_DIR/status-smoke-vault" --repo-root "$REPO_DIR" --obsidian --obsidian-skip-downloads
python3 scripts/wiki_lint.py "$RUN_DIR/status-smoke-vault" --obsidian --fail-on p1
python3 scripts/wiki_status.py "$RUN_DIR/status-smoke-vault" --write-dashboard
python3 scripts/wiki_status.py "$RUN_DIR/status-smoke-vault" --write-dashboard --force
python3 scripts/wiki_status.py "$RUN_DIR/status-smoke-vault" --write-dashboard --output "$RUN_DIR/outside.md"
python3 scripts/wiki_status.py "$RUN_DIR/status-smoke-vault" --write-dashboard --output sources/status.md
uv sync --dev --locked
uv run python scripts/check_quality.py
uv run python scripts/wiki_lint.py examples/minimal-vault --fail-on p1
uv run python scripts/wiki_status.py examples/minimal-vault
uv run python scripts/wiki_eval.py
bash -n setup.sh
git diff --check
uv run python -m skills_ref.cli validate skills/wiki-ingest
uv run python -m skills_ref.cli validate skills/query-writeback
uv run python -m skills_ref.cli validate skills/wiki-lint

Results:

All required checks passed.
Expected refusal: existing dashboard is not overwritten without --force.
Expected refusal: dashboard output outside the vault is rejected.
Expected refusal: dashboard output under sources/ is rejected.

Safety review

• No project output was written outside LLM-Wiki.
• deepseek_paper/ was not modified.
• raw/ evidence was not modified after ingest/copy.
• No human/science review approval was fabricated.
• No writeback approval gate was bypassed.
• No cloud/API path was used without explicit approval.
• This PR fixes one issue only.

Out-of-scope findings

• Full DeepSeek corpus validation was not run because this PR only addresses issue 增强 Obsidian + Claude 工作体验：命令入口、上下文面板、任务流与安全写入 #62's Obsidian/Agent workflow layer.
• Graph export runtime implementation remains separate from the graph-export prompt template.
• Query writeback runtime behavior was not redesigned.