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scripts/smoke-branch-conflicts.js","smoke:id-repair":"npm run build && node scripts/smoke-id-repair.js","smoke:command-docs":"npm run build && node scripts/smoke-command-docs.js","smoke:spike":"npm run build && node scripts/smoke-spike.js","smoke:goal-lifecycle":"npm run build && node scripts/smoke-goal-lifecycle.js","smoke:semantic-refs":"npm run build && node scripts/smoke-semantic-refs.js","smoke:checkpoint-templates":"npm run build && node scripts/smoke-checkpoint-templates.js","smoke:handoff":"npm run build && node scripts/smoke-handoff.js","smoke:warning-ux":"npm run build && node scripts/smoke-warning-ux.js","smoke:integration-ux":"npm run build && node scripts/smoke-integration-ux.js","docs:generate":"npm run build && node scripts/generate-docs-reference.js --write && node scripts/generate-release-notes-data.js --write","docs:release-notes":"node scripts/generate-release-notes-data.js --write","docs:release-notes:check":"node scripts/generate-release-notes-data.js --check","docs:check":"npm run build && node scripts/generate-docs-reference.js --check && node scripts/generate-release-notes-data.js --check && node scripts/check-doc-command-examples.js","docs:check-commands":"npm run build && node scripts/check-doc-command-examples.js","smoke:mdkg-dev":"npm run build && node scripts/smoke-mdkg-dev.js","smoke:mdkg-dev-docs":"npm run build && node scripts/smoke-mdkg-dev-docs.js","smoke:mdkg-dev-seo":"npm run build && node scripts/smoke-mdkg-dev-seo.js","smoke:mdkg-dev-polish-pass2":"npm run build && node scripts/smoke-mdkg-dev-polish-pass2.js","smoke:mdkg-dev-polish-pass3":"npm run build && node scripts/smoke-mdkg-dev-polish-pass3.js","smoke:mdkg-dev-polish-pass4":"npm run build && node scripts/smoke-mdkg-dev-polish-pass4.js","smoke:mdkg-dev-polish-pass5":"npm run build && node scripts/smoke-mdkg-dev-polish-pass5.js","smoke:mdkg-dev-a11y":"npm run build && node scripts/smoke-mdkg-dev-a11y.js","smoke:mdkg-dev-perf":"npm run build && node scripts/smoke-mdkg-dev-perf.js","smoke:demo-graph":"npm run build && node scripts/smoke-demo-graph.js","smoke:bundle":"npm run build && node scripts/smoke-bundle.js","smoke:graph-clone":"npm run build && node scripts/smoke-graph-clone.js","smoke:mcp":"npm run build && node scripts/smoke-mcp.js","smoke:bundle-import":"npm run smoke:subgraph","smoke:visibility":"npm run build && node scripts/smoke-visibility.js","smoke:sqlite":"npm run build && node scripts/smoke-sqlite.js","smoke:parallel":"npm run build && node scripts/smoke-parallel.js","smoke:goal":"npm run build && node scripts/smoke-goal.js","cli:snapshot":"npm run build && node scripts/cli_help_snapshot.js","cli:check":"npm run build && node scripts/cli_help_snapshot.js --check","cli:contract":"npm run build && node scripts/generate-command-contract.js --check","ci:release":"npm run test && npm run cli:check && npm run cli:contract && npm run docs:check && npm run smoke:git-materialize && npm run smoke:loop && npm run security:verify && node scripts/assert-publish-ready.js","prepack":"npm run build && npm run security:verify && node scripts/assert-publish-ready.js","prepublishOnly":"npm run test && npm run cli:check && npm run cli:contract && npm run docs:check && node dist/cli.js validate && npm run security:verify && npm run smoke:consumer && npm run smoke:git-materialize && npm run smoke:loop && npm run smoke:matrix && npm run smoke:upgrade && npm run smoke:init && npm run smoke:capabilities && npm run smoke:db && npm run smoke:db-queue && npm run smoke:db-queue-cli && npm run smoke:db-events && npm run smoke:db-materializer && npm run smoke:db-snapshot && npm run smoke:archive-work && npm run smoke:work-invocation && npm run smoke:cli-ux-polish && npm run smoke:operator-health && npm run smoke:fix-plan && npm run smoke:branch-conflicts && npm run smoke:id-repair && npm run smoke:command-docs && npm run smoke:spike && npm run smoke:goal-lifecycle && npm run smoke:semantic-refs && npm run smoke:checkpoint-templates && npm run smoke:handoff && npm run smoke:warning-ux && npm run smoke:integration-ux && npm run smoke:mdkg-dev && npm run smoke:mdkg-dev-docs && npm run smoke:mdkg-dev-seo && npm run smoke:mdkg-dev-polish-pass2 && npm run smoke:mdkg-dev-polish-pass3 && npm run smoke:mdkg-dev-polish-pass4 && npm run smoke:mdkg-dev-polish-pass5 && npm run smoke:mdkg-dev-a11y && npm run smoke:mdkg-dev-perf && npm run smoke:demo-graph && npm run smoke:bundle && npm run smoke:graph-clone && npm run smoke:mcp && npm run smoke:subgraph && npm run smoke:visibility && npm run smoke:sqlite && npm run smoke:parallel && npm run smoke:goal && node scripts/assert-publish-ready.js","postinstall":"node scripts/postinstall.js","smoke:subgraph":"npm run build && node 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project memory for AI coding agents","maintainers":[{"name":"nickreames","email":"nickreamesdev@gmail.com"}],"readme":"# mdkg\n\nMarkdown Knowledge Graph (`mdkg`) is Git-native project memory for AI coding agents: structured Markdown, deterministic context packs, handoffs, checkpoints, and validation.\n\nIt is built for:\n- human builders who want project truth and task state in git\n- AI agents that need deterministic context instead of ad-hoc file reading\n- human + agent pairs who want one shared source of truth\n\nmdkg stays deliberately boring:\n- repo-native under `.mdkg/`\n- TypeScript + Node.js `>=24.15.0`\n- zero third-party runtime dependencies\n- first-class rebuildable SQLite cache through built-in `node:sqlite`\n- no daemon, hosted index, or vector DB\n\nCurrent package version in source: `0.5.2`\n\nmdkg is still pre-v1 public alpha software. The public package is usable, but graph, cache, bundle, and DAL contracts may continue to change quickly while the project converges on a stable v1 surface.\n\n## mdkg.dev launch workspace\n\nThis repo now owns the prelaunch mdkg.dev source layout:\n\n- `mdkg-dev/` is the Astro static-site subproject for the canonical public site.\n- `docs/` is the Starlight docs subproject and repo-first documentation source plus generated command-reference output.\n- `examples/` contains local demo/template mdkg graphs for agentic coding and mdkg.dev website-generation demos.\n\nThese surfaces are intentionally excluded from the npm package payload. They are source and launch-readiness assets, not runtime CLI dependencies. The launch gates are local and deterministic:\n\n```bash\nnpm run docs:check\nnpm run smoke:mdkg-dev\nnpm run smoke:mdkg-dev-docs\nnpm run smoke:mdkg-dev-seo\nnpm run smoke:demo-graph\n```\n\nThe canonical site remains `mdkg.dev`. Demo graphs and preview deploys are separate from canonical SEO; durable `demo-N.mdkg.dev` promotion and any production deployment require explicit later approval.\n\n## The product shape\n\nmdkg has one core job: make repo knowledge cheap to retrieve and safe to reuse.\n\nThe primary loop is:\n1. initialize the repo\n2. create or select work\n3. inspect the current truth\n4. build a deterministic pack\n5. validate before closing the loop\n\nIf an agent is involved, use `mdkg pack <id>` for deterministic context and\n`mdkg handoff create <id-or-qid> --json` for a sanitized, copy-ready agent\nhandoff prompt. Handoffs summarize goal/work state, included pack nodes, latest\ncheckpoint, boundaries, required checks, next actions, and raw-content marker\nwarnings without copying raw node bodies into the prompt.\nIf a repo needs repeatable procedures, author them as first-class skills under `.mdkg/skills/`.\n\nWork nodes can separate semantic background from executable scope with\n`context_refs` and `evidence_refs`. Use `context_refs` for related plans,\nexternal docs, subgraph qids, or URI references that explain why work exists.\nUse `evidence_refs` for proof, audit, receipt, checkpoint, archive, or URI\nreferences. These fields are indexed, validated, shown, and packable, but they\ndo not make referenced nodes actionable goal work; keep executable queues in\ngoal `scope_refs`.\n\n## Install\n\n```bash\nnpm install -g mdkg\nmdkg --version\n```\n\nThe npm global install path is the canonical public-alpha path covered by release validation. One-off runners and other package managers may be useful in local tooling, but verify them before documenting them for a team.\n\n## Quickstart\n\nInitialize mdkg in a repo:\n\n```bash\nmdkg init --agent\nmdkg index\n```\n\nThis is the canonical AI-agent bootstrap path. It creates `.mdkg/`, `AGENT_START.md`, `AGENTS.md`, `CLAUDE.md`, `llms.txt`, `CLI_COMMAND_MATRIX.md`, strict-node `SOUL.md` / `COLLABORATION.md`, legacy `HUMAN.md` for one release, the default mdkg usage skills, `events.jsonl`, the skill registry, core pin updates, and configured skill mirrors under `.agents/skills/` and `.claude/skills/` by default. It also updates `.gitignore` / `.npmignore` by default. Use `--no-update-ignores` to opt out of those ignore-file updates.\n\nRun `mdkg index` after a fresh init before using `mdkg status --json` or\n`mdkg doctor --strict --json` as health gates. Init writes source scaffold\nfiles; indexing creates the generated graph, skill, capability, subgraph, and\nSQLite caches that strict doctor expects.\n\nFor a non-agent markdown graph only, run `mdkg init`.\n\nPreview safe scaffold upgrades in an existing mdkg workspace:\n\n```bash\nmdkg upgrade\nmdkg upgrade --json\n```\n\nApply only after reviewing the receipt:\n\n```bash\nmdkg upgrade --apply\n```\n\nUpgrade is intentionally conservative. It creates missing managed startup docs and templates, updates unchanged mdkg seed assets, and preserves customized docs, templates, skills, and core files as reported preserved customizations. Review `safe_to_apply`, `will_write_paths`, and `apply_side_effects` in the JSON receipt before applying. Agent-enabled workspaces can receive safe default skill upgrades and skill mirror refreshes; ignored event logs are skipped with guidance to run `mdkg event enable` if provenance should be restored.\n\nOlder workspaces can continue to inspect and validate current graph nodes before applying an upgrade. When local templates are missing for newly introduced built-in mdkg types, mdkg uses the installed package's bundled templates as a read-only schema fallback and warns that `mdkg upgrade --apply` can vendor the missing templates.\n\nCreate a task:\n\n```bash\nmdkg new task \"bootstrap cli\" --status todo --priority 1 --tags cli,build\n```\n\nCreate a recursive goal for long-running agent work:\n\n```bash\nmdkg new goal \"reach prepublish readiness\"\nmdkg goal show goal-1 --json\nmdkg goal next goal-1\nmdkg goal evaluate goal-1 --json\n```\n\nGoal nodes capture a measurable end condition, recursive loop state, required skills, required checks, and completion evidence. They guide agent harnesses through repeated graph-backed progress, while tasks, bugs, tests, spikes, and features remain the concrete executable work units. In this release `mdkg goal evaluate` is report-only: it lists required checks and evidence state, but does not execute scripts.\n\nCreate a research spike when the next useful work is investigation, planning,\nor grounding a future implementation:\n\n```bash\nmdkg new spike \"research mdkg.dev launch guide\" --status todo --priority 1\nmdkg task start spike-1\nmdkg show spike-1\n```\n\nSpikes are task-like work nodes, not autonomous research agents. mdkg does not\nperform web search, execute research, create follow-up nodes, or generate\n`SKILL.md` files automatically. Record sources, findings, tradeoffs,\nrecommendations, follow-up node ideas, and skill candidates in the spike body,\nthen create follow-up work intentionally:\n\n```bash\nmdkg new task \"write mdkg.dev quickstart guide\" --parent spike-1 --status todo --priority 1\nmdkg new test \"validate mdkg.dev docs examples\" --parent spike-1 --status todo --priority 1\nmdkg new task \"author mdkg.dev launch planning skill\" --parent spike-1 --status todo --priority 2\n```\n\nCreate an agent workflow document with a semantic portable id:\n\n```bash\nmdkg new manifest \"image worker\" --id agent.image-worker\nmdkg new work \"generate image\" --id work.generate-image\n```\n\nInspect the current truth:\n\n```bash\nmdkg search \"pack\"\nmdkg show task-1\nmdkg next\n```\n\nBuild deterministic context:\n\n```bash\nmdkg pack task-1\nmdkg pack task-1 --profile concise --dry-run --stats\nmdkg pack task-1 --visibility public --dry-run\nmdkg pack task-1 --edges context_refs,evidence_refs --format json\n```\n\nCreate a full `.mdkg` graph snapshot bundle for root or child orchestration:\n\n```bash\nmdkg archive compress --all\nmdkg archive verify --json\nmdkg bundle create --profile private\nmdkg bundle verify .mdkg/bundles/private/all.mdkg.zip\nmdkg bundle list --json\n```\n\nBundles are explicit graph transport artifacts, separate from task context packs. Before a commit in repos that track archives or bundles, refresh compressed archive caches first, then create the private bundle so the committed graph state is self-consistent. Private bundles are the default and may be committed in private repos when configured. Public bundles require at least one selected workspace with `visibility: public` and include only public workspace content and public archive sidecars; bundle creation fails if public content points at private graph, archive, or subgraph records.\n\nClone or fork a reusable graph template into a separate target when the target\nshould preserve IDs as its own graph namespace:\n\n```bash\nmdkg graph clone .mdkg/bundles/private/all.mdkg.zip --target demos/demo-1 --json\nmdkg graph fork templates/website-template-mdkg --target demos/live-build --start-goal goal-1 --json\n```\n\nImport a template graph into the current repo only through the rewritten-ID\npath. Review the dry-run receipt first, then apply explicitly:\n\n```bash\nmdkg graph import-template templates/website-template-mdkg --start-goal goal-1 --select-goal --dry-run --json\nmdkg graph import-template templates/website-template-mdkg --start-goal goal-1 --select-goal --apply --json\n```\n\n`graph clone` and `graph fork` preserve IDs; `graph import-template` rewrites\ncanonical numeric IDs and internal links to avoid same-repo collisions. With\n`--select-goal --apply`, import-template activates the rewritten imported start\ngoal, pauses competing active root goals, validates the graph, and then writes\nselected-goal state. Subgraphs remain read-only planning views; use\n`mdkg graph ...` when authored graph state should be created.\n\nRegister a child repo bundle as a read-only subgraph planning view:\n\n```bash\nmdkg subgraph add child_repo .mdkg/bundles/private/subgraphs/child_repo.mdkg.zip --source-path projects/child_repo\nmdkg subgraph list --json\nmdkg search \"child capability\"\nmdkg show child_repo:work.example\nmdkg pack child_repo:work.example --dry-run --stats\nmdkg capability resolve \"child capability\" --json\nmdkg subgraph verify child_repo --json\nmdkg subgraph audit child_repo --target .mdkg/subgraphs --json\nmdkg subgraph upgrade-plan child_repo --json\n```\n\nWhen the child repo is available under a configured root-relative `source_path`, refresh the root-owned bundle snapshot explicitly:\n\n```bash\nmdkg subgraph sync child_repo --dry-run --json\nmdkg subgraph sync child_repo --json\n```\n\n`audit` is read-only and reports source-path Git state, dirty tracked child files, bundle validity/freshness, root-owned bundle-path safety, optional materialized-target marker safety, and count-only capability summaries. `upgrade-plan` is also read-only, returns `apply_supported: false`, and proposes safe sync/verify/materialize next steps without writing bundles or child files.\n\n`sync` inspects the child Git repo, refuses dirty tracked changes by default, builds the configured private/public bundle into the root-owned source path, verifies it, and records `<branch>@<sha>` in `source_repo`. It never commits, pulls, pushes, checks out, resets, or mutates child mdkg Markdown. Use `--allow-dirty` only when the dirty state is intentional and must be recorded in the receipt.\n\nGenerate a local read-only inspection tree when humans need to browse extracted child graph files:\n\n```bash\nmdkg subgraph materialize child_repo --target .mdkg/subgraphs --clean --gitignore --json\n```\n\nMaterialized trees are generated local state, ignored by graph indexing/search/validation/packing/bundles/SQLite hydration, and protected by a `.mdkg-materialized.json` marker before clean replacement.\n\nSubgraph nodes are projected under the subgraph alias, for example `child_repo:task-1`. They are available to `list`, `search`, `show`, `pack`, capability discovery, and `capability resolve`, but remain read-only; mutate the child repo and sync its root-owned bundle snapshot to change subgraph content. Root-authored relationship and reference fields can point at configured subgraph qids such as `child_repo:work.example`; local ownership fields such as `epic`, `parent`, `prev`, and `next` stay local-only. Stale subgraphs warn during planning reads and fail `mdkg subgraph verify`. Public or internal subgraphs must be backed by public bundle profiles; private subgraphs stay private planning context.\n\nUse `mdkg graph refs <id-or-qid> --json` to inspect inbound and outbound scope, context, evidence, blocker, related, and structural links for local or read-only subgraph qids without mutating either graph.\n\nUse low-level Git lifecycle receipts when an agent run needs to accept an exact\nsource revision, close out local mdkg state, or prove push readiness before an\nexplicit remote update:\n\n```bash\nmdkg git inspect --json\nmdkg git materialize --request materialize-request.json --json\nmdkg git clone git@github.com:org/repo.git --target worktrees/repo --branch main --json\nmdkg git fetch --remote origin --branch main --json\nmdkg git closeout --json\nmdkg git push-ready --remote origin --branch main --json\nmdkg git push --remote origin --branch main --stage-all --message \"agent checkpoint\" --json\n```\n\n`mdkg git` uses the system Git CLI. Authentication stays external through SSH,\ncredential helpers, `gh`, CI/runtime environment, or shell state; mdkg rejects\nembedded URL credentials and records only sanitized refs, hashes, policy names,\nand receipts. `materialize` accepts only strict\n`mdkg.git.materialize.request.v1` JSON, verifies the full target ref and\naccepted revision, and publishes a contained destination only after all checks\npass; see the [verified Git materialization\nguide](https://docs.mdkg.dev/advanced-alpha/git-materialization/). `closeout`\nvalidates mdkg state before writing static JSON and\nMarkdown receipts, and when the project DB participated it also seals the\nSQLite state and writes a deterministic dump. Treat real `mdkg git push` as an\napproval-gated operation in agent runtimes.\n\nLaunch a local read-only MCP server when an MCP-capable agent should inspect a\nspecific mdkg graph without receiving mutation tools:\n\n```bash\nmdkg mcp serve --stdio --root /path/to/repo\n```\n\nThe MCP surface is stdio-only in this release. It exposes read-only tools for\nstatus, workspace/subgraph listing, search, show, in-memory pack generation,\ngoal current/next, and validation. It does not expose task updates, goal\nactivation, graph import, queue, event, archive, format, SQL, shell, arbitrary\nfile reads, filesystem mutation, environment variables, or secret access.\nFuture mutation allowlists remain design work.\n\nValidate before handoff or commit:\n\n```bash\nmdkg validate\nmdkg handoff create <id-or-qid> --out .mdkg/handoffs/example.md\n```\n\nDiscover cached capability surfaces:\n\n```bash\nmdkg index\nmdkg capability list --kind skill --json\nmdkg capability search \"image worker\" --kind work --json\nmdkg capability show <id-or-qid-or-slug> --json\nmdkg manifest list --json\nmdkg manifest show <id-or-qid-or-alias> --json\n```\n\n`MANIFEST.md` is optional. Repos with no manifest files still validate; when\npresent, manifest records describe reusable capability surfaces rather than\ngeneral planning notes. `SPEC.md` remains a legacy alias for one compatibility\nrelease, and `mdkg spec list/show/validate` remains a deprecated alias for\n`mdkg manifest list/show/validate`. `mdkg capability ...` remains the broader\nread-only discovery surface for skills, manifests, WORK contracts, core docs,\nand design docs.\n\nRegister source and artifact files as committed archive sidecars:\n\n```bash\nmdkg archive add ./inputs/key_input_doc.pdf --id archive.key-input-doc --kind source --visibility private\nmdkg archive verify archive://archive.key-input-doc\nmdkg archive list --json\n```\n\nCreate semantic mirror work contracts, orders, receipts, and artifacts:\n\n```bash\nmdkg work contract new \"generate image\" --id work.generate-image --agent-id agent.image-worker --kind image_generation --inputs prompt:text:required --outputs image_url:url:required\nmdkg work trigger work.generate-image --id order.generate-image-1 --requester user://example\nmdkg work order status order.generate-image-1 --json\nmdkg work receipt new \"generate image receipt\" --id receipt.generate-image-1 --work-order-id order.generate-image-1 --outcome success --receipt-status recorded\nmdkg work receipt verify receipt.generate-image-1 --json\nmdkg work artifact add receipt.generate-image-1 ./outputs/image.png --id archive.generated-image --kind artifact\n```\n\nCreate a manual order instead of a trigger-created order when you need to supply\ninput refs at order creation time:\n\n```bash\nmdkg work order new \"generate image request\" --id order.generate-image-manual --work-id work.generate-image --requester user://example --input-refs archive://archive.key-input-doc\n```\n\nReceipt statuses are `recorded`, `verified`, `rejected`, and `superseded`.\nUpdate and artifact commands accept local ids or local qids; subgraph qids are read-only and must be changed in their source workspace.\n\nUpdate structured task state and evidence while keeping body and narrative edits in markdown:\n\n```bash\nmdkg task start task-1 --run-id run_local_1\nmdkg task update task-1 --add-artifacts tests://unit.txt --add-tags release\nmdkg task done task-1 --checkpoint \"release readiness milestone\"\nmdkg task done task-1 --checkpoint \"goal complete\" --checkpoint-kind goal-closeout\n```\n\nCheckpoint kinds are `implementation`, `test-proof`, `goal-closeout`, `audit`, and `handoff`; generated checkpoint bodies include command evidence, pass/fail status, known warnings, changed surfaces, boundaries, and follow-up refs.\n\nEnsure and append baseline event memory:\n\n```bash\nmdkg event enable\nmdkg event append --kind RUN_COMPLETED --status ok --refs task-1 --notes \"manual closeout\"\n```\n\nCreate a first-class skill:\n\n```bash\nmdkg skill new release-readiness \"release readiness audit\" --description \"use when preparing a release\"\nmdkg skill list\nmdkg skill show release-readiness\nmdkg skill validate release-readiness\n```\n\n## LLM-readable onboarding artifacts\n\nThe root docs below are the canonical fast-start set for humans and agents:\n- [`AGENT_START.md`](AGENT_START.md)\n- [`llms.txt`](llms.txt)\n- [`PACK_EXAMPLES.md`](PACK_EXAMPLES.md)\n- [`CLI_COMMAND_MATRIX.md`](CLI_COMMAND_MATRIX.md)\n- [`COVERAGE_HARDENING_MATRIX.md`](COVERAGE_HARDENING_MATRIX.md)\n- [`CHANGELOG.md`](CHANGELOG.md)\n- [`CONTRIBUTING.md`](CONTRIBUTING.md)\n\n## Repository shape\n\nmdkg lives under a hidden root directory:\n- `.mdkg/core/` rules and pinned docs\n- `.mdkg/design/` product, design, and decision docs\n- `.mdkg/work/` tasks, bugs, tests, spikes, epics, checkpoints\n- `.mdkg/templates/` templates used by `mdkg new`\n- `.mdkg/skills/` Agent Skills packages\n- `.mdkg/archive/` sidecar metadata plus deterministic compressed source/artifact caches\n- `.mdkg/bundles/` optional committed full graph snapshot bundles\n- `.mdkg/index/mdkg.sqlite` optional committed, rebuildable SQLite access cache\n- `.mdkg/index/subgraphs.json` generated read-only subgraph projection cache\n- `.mdkg/db/` future project application database layout and receipts\n- `.mdkg/subgraphs/` generated materialized subgraph inspection trees\n- `.agents/skills/` Codex/OpenAI-facing mirrored skills\n- `.claude/skills/` Claude-facing mirrored skills\n- `.mdkg/index/*.json` generated JSON compatibility cache files\n\n## Primary commands\n\nThese are the commands new users and agents should learn first:\n- `mdkg init`\n- `mdkg upgrade`\n- `mdkg new`\n- `mdkg search`\n- `mdkg show`\n- `mdkg next`\n- `mdkg pack`\n- `mdkg skill`\n- `mdkg capability`\n- `mdkg spec`\n- `mdkg archive`\n- `mdkg work`\n- `mdkg goal`\n- `mdkg task`\n- `mdkg validate`\n- `mdkg status`\n- `mdkg mcp`\n- `mdkg fix`\n\nAdvanced / maintenance commands still exist, but they are not the first-run story:\n- `mdkg event`\n- `mdkg checkpoint`\n- `mdkg index`\n- `mdkg guide`\n- `mdkg format`\n- `mdkg doctor --strict --json`\n- `mdkg fix plan --json`\n- `mdkg workspace`\n\nFor large historical graphs, use `mdkg validate --changed-only --json` to keep\nwarning review focused on changed `.mdkg` files while full graph errors still\nrun. Use `mdkg validate --summary --json --limit 20` for bounded agent or CI\nlogs, and add `--json-out <path>` when a clean full JSON receipt should be\nwritten as an artifact. Use\n`mdkg format --headings --dry-run --summary --json --limit 20` to review missing\nrecommended heading additions with bounded output before applying them with\n`--apply`.\n\n## Operator health\n\nUse `mdkg status --json` for a read-only operator summary before mutating a\nrepo. It reports package/release state, Git cleanliness, graph validity,\nselected-goal state, project DB verification state, and generated cache\nfreshness without rebuilding indexes, running migrations, repairing files, or\nchanging selected-goal state.\n\nUse `mdkg doctor --strict --json` when a CI job or agent needs actionable\ntyped checks. Strict doctor keeps the existing diagnostic command read-only and\nadds stable check fields: `id`, `status`, `severity`, `message`,\n`remediation`, and optional `refs`. Strict mode fails on invalid graph state,\nstale generated graph/capability cache state, stale or achieved selected-goal\nstate, and enabled project DB verification failures. Warnings such as dirty\nruntime DB files, archive size guidance, and bundle handoff guidance remain\nwarnings unless their underlying check fails.\n\nUse `mdkg fix plan --json` when you want repair guidance without mutation. It\nemits a receipt-shaped plan for generated index/cache repair, missing graph\nreferences, and duplicate local ids. Planned changes include affected paths,\nrisk, reason codes, command hints, and per-change `apply_supported` metadata.\nDuplicate-ID graph repairs can be applied with\n`mdkg fix apply --family ids --json` or `mdkg fix ids --apply --json`; use\n`--base-ref main` when mainline IDs should win. Index/cache and graph-reference\nfindings remain review-only. For unresolved Git add/add conflicts, `fix ids`\nkeeps stage 2 at the conflicted path, rewrites stage 3 to the next unused\ncanonical ID/path, and records a receipt.\n\n## Skills\n\nmdkg supports Agent Skills as procedural memory.\n\nCanonical layout:\n\n```text\n.mdkg/skills/<slug>/SKILL.md\n```\n\nCurrent source behavior:\n- skills are indexed into `.mdkg/index/skills.json`\n- `.mdkg/skills/` remains the canonical skill source of truth\n- `.agents/skills/` and `.claude/skills/` are materialized mirrors for agent products\n- skills have a focused command family:\n  - `mdkg skill new <slug> \"<name>\" --description \"...\"`\n  - `mdkg skill list`\n  - `mdkg skill search \"<query>\"`\n  - `mdkg skill show <slug>`\n  - `mdkg skill validate [<slug>]`\n  - `mdkg skill sync`\n- machine-readable skill discovery and inspection is available through:\n  - `mdkg skill list --json`\n  - `mdkg skill search \"<query>\" --json`\n  - `mdkg skill show <slug> --json`\n  - `mdkg skill list --xml|--toon|--md`\n  - `mdkg skill search \"<query>\" --xml|--toon|--md`\n  - `mdkg skill show <slug> --xml|--toon|--md`\n- work items may reference `skills: [slug,...]`\n- packs may include skills with `--skills` and `--skills-depth`\n- mdkg indexes and discovers skills but does not execute skill scripts\n- `SKILL.md` is canonical\n- `SKILLS.md` is tolerated on read for compatibility, but validation warns and canonical docs still use `SKILL.md`\n- if both `SKILL.md` and `SKILLS.md` exist in one skill folder, validation fails\n- `mdkg skill new` scaffolds `SKILL.md`, `references/`, `assets/`, and `scripts/` only when requested with `--with-scripts`\n- `mdkg skill sync` refreshes the product-specific mirrors from canonical `.mdkg/skills/`\n- mirrored skill folders are append-focused outputs; preserve unrelated existing folders and fail on same-slug collisions unless explicitly forced\n\nThis repo now dogfoods mdkg-authored internal skills:\n- `author-mdkg-skill`\n- `select-work-and-ground-context`\n- `build-pack-and-execute-task`\n- `pursue-mdkg-goal`\n- `pursue-mdkg-loop`\n- `verify-close-and-checkpoint`\n\nOptional skill metadata with prefixes such as `ochatr_*` is treated as vendor extension data. Structured skill output exposes it under `extensions.ochatr` while keeping the top-level `ochatr` field as a compatibility alias introduced in 0.0.9. ochatr.ai is a pioneering adopter of this extension pattern, not the name of the base mdkg standard.\n\n## Capability cache\n\nmdkg maintains `.mdkg/index/capabilities.json` as a derived access cache for deterministic capability surfaces:\n- skills from `.mdkg/skills/**/SKILL.md`\n- canonical `MANIFEST.md` and legacy `SPEC.md`\n- `WORK.md`\n- core docs\n- design docs\n\nThe capability cache is not the full graph and is not source of truth. Normal tasks, epics, bugs, tests, feats, and checkpoints remain in the standard graph index. Markdown remains authoritative; deleting the cache is recoverable with `mdkg index` or by running a capability command when auto-reindex is enabled.\n\nCapability records aggregate enabled registered workspaces and include deterministic source metadata such as `workspace`, `visibility`, `kind`, `id`, `qid`, `path`, headings, refs, source hash, and `indexed_at`. MANIFEST/SPEC and WORK records also expose read-only `linkage` arrays when related work contracts, work orders, and receipts exist, so an orchestrator can discover a capability from reusable surface to invocation evidence without loading the full graph. Workspace `visibility` also feeds mdkg's export safety checks for public/internal packs and public bundles. This is a CLI safety layer, not secret scanning, body redaction, or a replacement for private git hosting.\n\n## Index backends and parallel safety\n\nFresh `mdkg init` workspaces default to `index.backend: sqlite`, which writes `.mdkg/index/mdkg.sqlite` as a rebuildable access cache using Node's built-in `node:sqlite`. Existing workspaces that are migrated from older configs default to `index.backend: json` until they opt in. Markdown files, archive sidecars, bundle manifests, and config remain source of truth in both modes.\n\n`mdkg index` still writes JSON compatibility caches (`global.json`, `skills.json`, `capabilities.json`, and subgraph projections when configured). In SQLite mode it also rebuilds the SQLite cache with nodes, edges, skills, capabilities, archive metadata, subgraphs, source hashes, and schema metadata. Deleting the SQLite file is recoverable with `mdkg index`.\n\nGraph ingestion is bounded before Markdown bodies are read. New workspaces expose\n`index.limits.max_files`, `max_file_bytes`, `max_total_bytes`, and `max_depth` in\n`.mdkg/config.json`; older configs receive the same conservative defaults in\nmemory. Pack traversal and body reads are bounded before construction, ZIP input\nis bounded before allocation and inflation, and the local read-only MCP server\nrejects oversized lines, batches, nesting, bodies, tool payloads, and responses.\n\nMutating commands use a workspace mutation lock plus atomic writes. SQLite mode additionally reserves numeric ids in a SQLite transaction before writing Markdown so parallel `mdkg new` and checkpoint calls avoid naming conflicts. Skipped ids after failed writes are acceptable because Markdown remains canonical.\n\n## Project DB Layout\n\n`.mdkg/db` is reserved for project application database state, separate from\nthe rebuildable `.mdkg/index` graph cache. Run `mdkg db init` to create the\ngeneric scaffold and explicitly enable `db.enabled` in config. The generic\nlayout is `.mdkg/db/schema`, `.mdkg/db/runtime`, `.mdkg/db/state`, and\n`.mdkg/db/receipts`; `mdkg db init` also writes a deterministic\n`.mdkg/db/project-db.json` manifest.\n\nRuntime DB files, WAL, SHM, journal, lock, and temp files are ignored by\ndefault. `mdkg db init` does not create an active runtime SQLite database.\nRun `mdkg db migrate` after init to create or update the active runtime\nSQLite database at the configured `db.runtime_path`; built-in migrations write\nmdkg-owned generic foundation tables, public local node:sqlite queue delivery\ntables, internal local event/receipt/reducer tables, writer lease/CAS tables,\nand queue control state, then record migration order, checksums, and applied\ntimestamps. Queue state is durable local delivery infrastructure, not canonical\nevent history. Use `mdkg db queue create|pause|resume|enqueue|claim|ack|fail|dead-letter|release-expired|stats|list|show`\nto operate local project queues. Paused queues reject enqueue/claim while still\nallowing ack/fail/dead-letter/release-expired so leased work can settle. Event\nrows are durable local project DB history; receipts, reducers, writer leases,\nand materializers remain internal helper surfaces in this release, with no\npublic `mdkg db event`, `mdkg db reducer`, `mdkg db lease`, or\n`mdkg db materializer` CLI yet.\n`mdkg db queue contract --json` is the read-only public adapter contract for\ndownstream integrations. It documents canonical payload hashing, dedupe keys,\noldest-ready claim order, lease-owner checked ack/fail/dead-letter, retry\ndelay, expired lease reclaim, max-attempt dead-letter behavior, pause/resume,\nsnapshot queue policy, and stats without exposing raw SQL or making queue rows\ncanonical runtime history.\n`mdkg work trigger --enqueue <queue>` can bridge a submitted work order mirror\ninto an explicitly created active project DB queue; it writes local delivery\nstate only and never executes work.\nUse `mdkg db verify` for non-mutating health checks over config, layout,\nruntime SQLite integrity, migration metadata, and transient runtime files. Use\n`mdkg db stats` for deterministic table counts, DB size, migration state,\nreceipt-file count, and state snapshot presence.\nUse `mdkg db snapshot seal` to create an explicit sealed checkpoint at\n`.mdkg/db/state/project.sqlite` with `.mdkg/db/state/project.manifest.json`.\nThe default queue policy is `--queue-policy drain`, which requires no ready or\nleased queue messages. Use `--queue-policy paused` only when ready messages are\nintentionally preserved in paused queues; leased messages always block sealing.\nUse `mdkg db snapshot verify` and `mdkg db snapshot status` for checkpoint\nhealth, and use `mdkg db snapshot dump` / `mdkg db snapshot diff` as\ndeterministic review aids for SQLite snapshots instead of comparing raw binary\nbytes.\nSchema files, manifests, receipt artifacts, and opt-in sealed snapshots remain\ncommit-eligible by explicit repo policy. `mdkg doctor` warns when active runtime\nor transient project DB files are present so they are not accidentally committed\nas sealed state.\n\n## Goal nodes\n\nGoal nodes are durable recursive objective contracts. Use `mdkg new goal \"<objective>\"` when a human or agent needs to keep working across multiple concrete nodes until a measurable end condition is achieved.\n\n`goal` is work-like but distinct from `task`: it can have status, priority, graph links, skills, explicit `scope_refs`, and structured goal fields, but normal `mdkg next` does not select goals. Use `mdkg goal activate <goal-id>` to make one local root goal active, pause competing local active goals, and select it for future `goal next` calls. Use `mdkg goal select <goal-id>` only when you want to change the local ignored selected-goal pointer without changing lifecycle state. `mdkg goal next <goal-id>` remains available for explicit selection. Epics organize goal scope recursively but are not returned as executable work.\n\nUse `mdkg goal claim [goal-id] <work-id>` to durably set `active_node` after choosing the next scoped item. `goal next` is read-only. Use `mdkg goal pause|resume|done` to update goal state after review; closing a goal moves the final `active_node` to `last_active_node` so completed goals keep history without staying actionable. Use `mdkg goal archive` for superseded historical roadmap goals that should remain readable but non-actionable.\n\nRequired checks are stored as report-only guidance. Agents should run the checks themselves, record evidence in the goal or active work item, then use `mdkg goal evaluate` to summarize the current evidence state. During normal goal execution, skill improvements should be recorded as improvement candidates or proposal nodes; edit `SKILL.md` files only when the active node is explicit skill-maintenance work.\n\n## Loop nodes\n\nLoop nodes are durable declarative process state for reusable agentic workflows. Use `mdkg new loop \"<process>\"` for a loop record, or `mdkg loop fork <template> --scope <scope>` to instantiate a seeded template for a concrete repo, folder, or goal.\n\n`loop` is one first-class node type. A loop can act as a reusable template, scoped fork, or run-bearing loop through metadata and links; mdkg does not create separate `loop_template` or `loop_run` node types in this release. Loop metadata records mode, scope, lineage, materialization mode, child refs, run/evidence refs, definition of done, and blocker-continuation policy.\n\n`mdkg loop list|show|plan|runs` inspect loop state without executing agents. `mdkg loop fork` creates graph state; by default it materializes linked spike/task/test child nodes, while `--planning-only` or `--no-children` creates only the scoped loop shell. mdkg defines reusable process state and graph context; omni-room-runtime or another runtime owns agent/tool execution, sandboxes, traces, and model routing.\n\n## Research spikes\n\nSpikes are first-class actionable work nodes for research and planning. Use\n`mdkg new spike \"<question>\"` when the right output is a documented\nrecommendation, not code. They share the existing task lifecycle:\n\n```bash\nmdkg new spike \"research queue-backed materializer UX\" --status todo --priority 1\nmdkg task start spike-1\nmdkg task update spike-1 --status review --add-refs task-250\nmdkg task done spike-1\n```\n\nThe default spike template includes sections for research question, context,\nsearch plan, findings, options and tradeoffs, recommendation, follow-up nodes,\nskill candidates, data-structure and algorithm notes, UX notes, security notes,\nmdkg.dev launch implications, and evidence/sources.\n\nSpikes deliberately do not expose a `mdkg spike ...` namespace in this release,\ndo not run browser or web-search tools, do not create tasks/tests/goals, and do\nnot write `SKILL.md` files. They make the research output reviewable so humans\nor agents can intentionally create the next nodes with normal mdkg commands.\n\n## Agent workflow files\n\nmdkg recognizes a small set of canonical agent workflow documents:\n- `MANIFEST.md` for agent, package, or runtime capability manifests\n- `WORK.md` for reusable work contracts\n- `WORK_ORDER.md` for concrete requests against work contracts\n- `RECEIPT.md` for completed work output and artifacts\n- `FEEDBACK.md`, `DISPUTE.md`, and `PROPOSAL.md` for review loops\n\nUse `mdkg new manifest|work|work_order|receipt|feedback|dispute|proposal \"<title>\"` to scaffold them. `mdkg new spec` remains a deprecated alias that emits `MANIFEST.md` during the compatibility bridge. `--id <portable-id>` is available for these types when semantic ids such as `agent.image-worker` or `work.generate-image` are preferred.\n\nRelational templates contain editable placeholder refs. `manifest` and `work` scaffold as validation-clean standalone docs; `work_order`, `receipt`, `feedback`, `dispute`, and `proposal` need real refs before strict `mdkg validate` passes.\n\nFor executable or purchasable capability mirrors, prefer the lifecycle helpers under `mdkg work ...`. They create and update `WORK.md`, `WORK_ORDER.md`, and `RECEIPT.md` semantic mirror files only. `mdkg work trigger` creates a deterministic submitted `WORK_ORDER.md` from a WORK contract or a MANIFEST with exactly one resolvable work contract; legacy SPEC refs remain supported during the compatibility bridge. `mdkg work order status` and `mdkg work receipt verify` are read-only review helpers for deterministic closeout. `mdkg work validate [<id-or-qid>] [--type manifest|spec|work|work_order|receipt|feedback|dispute|proposal] [--profile omni-room] --json` is a read-only focused validator for agent workflow mirrors; it returns typed diagnostics and warns on obvious raw secret, prompt, token, or payload markers. `mdkg validate --profile omni-room` and `mdkg work validate --profile omni-room` apply explicit profile checks after generic validation.\n\nOptional contract-profile fields are generic semantic mirrors, not runtime execution state. `contract_profile` is accepted on MANIFEST, WORK, WORK_ORDER, and RECEIPT surfaces; `validation_policy_ref` and `evidence_policy_ref` are accepted on MANIFEST, WORK_ORDER, and RECEIPT; `receipt_kind` and `redaction_class` are RECEIPT-only. These fields are separate from MANIFEST `resource_profile`, WORK `kind`, WORK_ORDER `artifact_policy`, RECEIPT `redaction_policy`, and pack/bundle `--profile` flags. Generic validation accepts well-shaped custom profile, kind, and class values with warnings; explicit `--profile omni-room` validation escalates unknown or incompatible values. Bare `profile` is intentionally ambiguous and is diagnosed rather than treated as an alias.\n\n`mdkg work trigger --enqueue <queue>` optionally writes a local project DB queue delivery message after the queue has been explicitly created and is active; it still does not execute work. Production order state, receipt state, feedback, disputes, payments, ledgers, marketplace inventory, fulfillment records, and execution state remain canonical outside mdkg, such as in Postgres or another application database. Omni Room and other downstream runtimes own runtime policy, queue execution, final receipt normalization, and downstream adoption. Do not store raw secrets, credentials, live payment state, ledger mutations, canonical marketplace state, or bulky raw payloads in these mirrors.\n\n## Archive sidecars\n\nArchive entries live under `.mdkg/archive/<archive.id>/` and are normal graph nodes with `type: archive`. `mdkg archive add` copies the source into a managed local `source/` directory, writes a frontmatter sidecar `<file>.md`, and writes a deterministic single-file ZIP cache `<file>.zip`. The original source path is left untouched.\n\nArchive sidecars support `archive://archive.example` refs from orders, receipts, artifacts, proof refs, and other workflow metadata. `artifact://...` refs remain external or runtime-managed artifact identities; `archive://...` refs name committed mdkg archive sidecars. `mdkg validate` and `mdkg archive verify` both require the sidecar contract, ZIP cache hash, readable ZIP payload, payload SHA-256, and payload byte size to match. A missing raw local source copy is non-fatal when the committed sidecar and ZIP cache are valid.\n\nWhen the source passed to `mdkg archive add` is inside the repo, `source_path` is repo-relative. Outside-repo sources are redacted to `external:<basename>` so sidecars do not leak absolute local paths.\n\nArchive sidecar visibility defaults to `private`. Use `mdkg archive add --visibility public` only when the sidecar metadata and ZIP cache are safe for public packs or public bundles.\n\nArchive compression follows workspace ownership. `mdkg archive compress --all`\ncompresses archives from enabled local workspaces and reports read-only imported\narchive projections as exclusions; it never treats bundle ZIP fragments as\nfilesystem paths. Use `--all --ws <local-alias>` to limit bulk compression or a\nworkspace-qualified qid such as `root:archive.example` for an exact local\ntarget. Direct imported qids and imported `--ws` aliases fail before writes with\nguidance to compress in the source workspace and refresh its subgraph bundle.\nThe JSON receipt preserves `action`, `count`, and `archives` and adds the\nrequested workspace, selected local workspaces, and excluded read-only qids.\n\nBy default, init/upgrade ignore generated raw archive source copies with `.mdkg/archive/**/source/`; sidecar `.md` files and compressed `.zip` caches remain commit-eligible. `mdkg doctor` warns when a committed archive ZIP cache exceeds `archive.large_cache_warning_bytes` in `.mdkg/config.json` (default `26214400`; set `0` to disable). Large-cache warnings do not block archive add or validation.\n\n## Current direction\n\nThis release includes:\n- `init --agent`\n- default ignore updates with `--no-update-ignores` for generated JSON index/temp/lock files, `.mdkg/pack/`, and raw archive source copies\n- root-only published init seed config\n- skills indexing and search/show/list support\n- JSON capability cache for skills, `MANIFEST.md` / legacy `SPEC.md`, `WORK.md`, core docs, and design docs\n- optional `mdkg manifest list/show/validate` for reusable manifest capability records, with `mdkg spec ...` retained as a legacy alias for one compatibility release\n- SQLite index backend for fresh workspaces using built-in `node:sqlite`\n- mutation locking and atomic writes for parallel mdkg calls\n- first-class `goal` nodes and `mdkg goal show/next/evaluate/pause/resume/done`\n- first-class `loop` nodes and `mdkg loop list/show/fork/plan/runs`\n- optional `skills: [...]` on work items\n- pack-time skill inclusion\n- latest-checkpoint resolver + index hint\n- events JSONL validation\n- XML / TOON / Markdown output for node and skill list/search/show\n- agent workflow file types and semantic `mdkg new --id` support\n- product-specific skill mirrors for Codex/OpenAI and Claude\n- shared `AGENT_START.md` startup guidance\n- conservative `mdkg upgrade` with mode-aware init manifests\n- archive sidecars with deterministic ZIP caches\n- semantic mirror helpers under `mdkg work ...`, including trigger/order status/receipt verification\n- explicit public/internal/private visibility enforcement for packs, bundles, archives, imports, validation, and doctor diagnostics\n- strict archive ZIP payload integrity checks during validation\n\nCurrent direction:\n- keep the OSS story generic around `mdkg init --agent`\n- use base `mdkg init` only for repos that do not want agent bootstrap assets\n- keep `pack <id>` at the center of the human/agent loop\n- use `mdkg task ...` for structured state changes and markdown edits for narrative/body content\n- make event logging guided instead of purely manual\n- dogfood real skills inside the repo\n- make skill authoring first-class through `mdkg skill`\n- make `CLI_COMMAND_MATRIX.md` the single source of truth for the live CLI surface\n- keep production execution databases canonical while mdkg stores committed semantic mirrors\n- run manual behavior audits before enforcing stronger coverage thresholds\n\nDesign and decision records live in the internal graph under `.mdkg/design/`.\n\n## Safety\n\nmdkg is not a secret store.\n\nUse these defaults:\n- keep generated `.mdkg/index/*.json`, temp, lock, WAL, SHM, and journal files gitignored\n- commit `.mdkg/index/mdkg.sqlite` only when the repo intentionally tracks a reasonably sized rebuildable access cache\n- keep `.mdkg/db/runtime/` and `.mdkg/db` WAL/SHM/journal/lock/temp files gitignored\n- commit `.mdkg/db/schema`, manifests, receipts, and sealed state snapshots only by explicit repo policy\n- keep `.mdkg/pack/` gitignored\n- keep `.mdkg/archive/**/source/` gitignored unless a repo intentionally commits raw local copies\n- commit archive sidecar `.md` metadata and deterministic `.zip` caches when they are needed for reviewable evidence\n- event logs are committed by default; ignore or delete them manually if a repo wants local-only provenance\n- do not ship `.mdkg/` into production builds or published packages\n- if an external orchestrator is writing mdkg state, keep one durable writer per run and batch commits at end-of-run or checkpoint boundaries\n- do not commit on every tool call\n\n## Contributing\n\nStart with [`CONTRIBUTING.md`](CONTRIBUTING.md). mdkg prefers Prompt Requests before Pull Requests: contributors can submit intent, workflows, prompts, and acceptance criteria without needing to write code first.\n\nThis repo dogfoods mdkg itself. The behavior source of truth is the combination of:\n- source under `src/`\n- tests under `tests/`\n- internal rules and design docs under `.mdkg/`\n\nSuggested local loop:\n1. create or select a work item\n2. inspect truth with `search`, `show`, or `next`\n3. build context with `pack <id>`\n4. mutate task state with `mdkg task ...` when durable state changes\n5. ensure event logging exists if the JSONL file was deleted or is missing\n6. implement and test\n7. run `mdkg validate`\n\n## License\n\nMIT\n","readmeFilename":"README.md"}