@goondocks/myco 0.27.18 → 1.0.0

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Files changed (13) hide show
  1. package/README.md +9 -6
  2. package/dist/ui/assets/index-DE6oYYru.css +2 -0
  3. package/dist/ui/assets/index-Doue33fQ.js +415 -0
  4. package/dist/ui/index.html +2 -2
  5. package/package.json +13 -13
  6. package/scripts/select-binary.mjs +23 -0
  7. package/skills/myco/SKILL.md +40 -50
  8. package/skills/myco/references/cli-usage.md +43 -88
  9. package/skills/myco/references/reconfiguration.md +47 -59
  10. package/skills/myco/references/vault-status.md +23 -42
  11. package/skills/myco/references/wisdom.md +2 -2
  12. package/dist/ui/assets/index-D80qRqAU.css +0 -2
  13. package/dist/ui/assets/index-Dri_UAax.js +0 -415
package/dist/ui/index.html CHANGED
@@ -5,8 +5,8 @@
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  <link rel="icon" type="image/svg+xml" href="/favicon.svg" />
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  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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  <title>Myco</title>
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- <script type="module" crossorigin src="/assets/index-Dri_UAax.js"></script>
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- <link rel="stylesheet" crossorigin href="/assets/index-D80qRqAU.css">
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+ <script type="module" crossorigin src="/assets/index-Doue33fQ.js"></script>
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+ <link rel="stylesheet" crossorigin href="/assets/index-DE6oYYru.css">
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  </head>
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  <body>
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  <div id="root"></div>
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
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2
  "name": "@goondocks/myco",
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- "version": "0.27.18",
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+ "version": "1.0.0",
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  "description": "Collective agent intelligence — Claude Code plugin",
5
5
  "type": "module",
6
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  "bin": {
@@ -59,35 +59,35 @@
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  "directory": "packages/myco"
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  },
61
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  "dependencies": {
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- "@anthropic-ai/claude-agent-sdk": "^0.3.143",
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- "@anthropic-ai/sdk": "^0.96.0",
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+ "@anthropic-ai/claude-agent-sdk": "^0.3.152",
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+ "@anthropic-ai/sdk": "^0.99.0",
64
64
  "@inquirer/prompts": "^8.4.2",
65
65
  "@modelcontextprotocol/sdk": "^1.28.0",
66
- "@openai/agents": "^0.11.4",
66
+ "@openai/agents": "^0.11.5",
67
67
  "chokidar": "^5.0.0",
68
68
  "gray-matter": "^4.0.3",
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- "semver": "^7.7.4",
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- "shell-quote": "^1.8.1",
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+ "semver": "^7.8.1",
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+ "shell-quote": "^1.8.4",
71
71
  "smol-toml": "^1.6.1",
72
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  "yaml": "^2.8.4",
73
73
  "zod": "^4.4.3"
74
74
  },
75
75
  "optionalDependencies": {
76
- "@goondocks/myco-darwin-arm64": "0.27.18",
77
- "@goondocks/myco-darwin-x64": "0.27.18",
78
- "@goondocks/myco-linux-x64": "0.27.18",
79
- "@goondocks/myco-linux-arm64": "0.27.18",
80
- "@goondocks/myco-windows-x64": "0.27.18"
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+ "@goondocks/myco-darwin-arm64": "1.0.0",
77
+ "@goondocks/myco-darwin-x64": "1.0.0",
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+ "@goondocks/myco-linux-arm64": "1.0.0",
79
+ "@goondocks/myco-linux-x64": "1.0.0",
80
+ "@goondocks/myco-windows-x64": "1.0.0"
81
81
  },
82
82
  "devDependencies": {
83
83
  "@goondocks/myco-shared": "*",
84
84
  "@types/bun": "^1.3.14",
85
- "@types/node": "^25.9.0",
85
+ "@types/node": "^25.9.1",
86
86
  "@types/semver": "^7.7.1",
87
87
  "@types/shell-quote": "^1.7.5",
88
88
  "@vscode/ripgrep": "^1.15.14",
89
89
  "sqlite-vec": "^0.1.8",
90
- "tsx": "^4.0.0",
90
+ "tsx": "^4.22.3",
91
91
  "typescript": "^6.0.3"
92
92
  }
93
93
  }
package/scripts/select-binary.mjs CHANGED
@@ -80,3 +80,26 @@ fs.writeFileSync(
80
80
  );
81
81
 
82
82
  process.stdout.write(`[myco] Selected platform binary: ${binaryPath}\n`);
83
+
84
+ // Self-install as a managed OS service so launchd / systemd starts the
85
+ // daemon at every login from the moment Myco is installed. Skipped in
86
+ // source checkouts (no published dist/), skipped silently on failure
87
+ // (the daemon's lazy-spawn path still works; doctor will surface the
88
+ // gap). Plan reference: Decision 13 / Step 12.
89
+ if (!isSourceCheckout) {
90
+ const distSelfInstall = path.join(pkgRoot, 'dist/src/service/self-install.js');
91
+ if (fs.existsSync(distSelfInstall)) {
92
+ try {
93
+ const mod = await import(distSelfInstall);
94
+ const stderrLogger = {
95
+ info: (kind, message) => process.stderr.write(`[myco] ${kind}: ${message}\n`),
96
+ debug: () => undefined,
97
+ warn: (kind, message) => process.stderr.write(`[myco] ${kind}: ${message}\n`),
98
+ error: (kind, message) => process.stderr.write(`[myco] ${kind}: ${message}\n`),
99
+ };
100
+ await mod.ensureSelfInstalledAsService(stderrLogger);
101
+ } catch (err) {
102
+ process.stderr.write(`[myco] Service install skipped: ${err?.message ?? err}\n`);
103
+ }
104
+ }
105
+ }
package/skills/myco/SKILL.md CHANGED
@@ -1,6 +1,6 @@
1
1
  ---
2
2
  name: myco
3
- description: Use when making design decisions, debugging non-obvious issues, encountering gotchas, wondering why code is structured a certain way, or when you need context about prior work on the same feature or component. Myco captures the reasoning, trade-offs, and lessons behind the codebase — things the code itself doesn't show. Also use when the user mentions vault, spores, sessions, team knowledge, institutional memory, or prior decisions.
3
+ description: Use when making design decisions, debugging non-obvious issues, encountering gotchas, wondering why code is structured a certain way, delegating work to another agent, or when you need context about prior work on the same feature or component. Myco captures the reasoning, trade-offs, and lessons behind the codebase — things the code itself doesn't show. Also use when the user mentions vault, spores, sessions, team knowledge, institutional memory, or prior decisions.
4
4
  ---
5
5
 
6
6
  # Myco — Collective Agent Intelligence
@@ -15,6 +15,7 @@ Use Myco tools proactively in these situations — don't wait to be asked:
15
15
  - **When debugging a non-obvious issue** — search for the error message, component name, or symptom. A prior session may have hit the same problem and documented the root cause.
16
16
  - **When wondering why code is structured a certain way** — decisions and trade-offs behind the architecture are captured as spores.
17
17
  - **When continuing work on a feature** — check session history and plan progress for context on what's been done and what's pending.
18
+ - **Before delegating work to another agent, subagent, teammate, worker session, or other spawned process** — refresh the current Cortex instructions and pass them along verbatim so delegated work sees the same Myco guidance.
18
19
  - **After discovering a gotcha, making a key decision, or fixing a tricky bug** — save it so future sessions benefit from the knowledge.
19
20
  - **When starting work on a branch** — context is injected automatically at session start, but you can call `myco_search` and then follow each result's `retrieve` hint for deeper context.
20
21
 
@@ -31,20 +32,18 @@ Use the CLI tool surface below for going deeper than the automatic context injec
31
32
 
32
33
  ## Setup
33
34
 
34
- If the vault isn't configured, run `myco init` in the project directory for guided first-time setup.
35
-
36
- For reconfiguration, status checks, and ongoing management, use the CLI commands and tool surfaces documented below. For detailed vault health checks, see `references/vault-status.md`.
35
+ Setup is automatic. Installing the global `myco` binary brings up the daemon and creates a default Grove; opening this project in any supported agent registers it on the first hook. For ongoing status checks and per-project overrides (portable Grove identity, dogfood binary pinning), use the dashboard's Symbionts page. For detailed vault health checks, see `references/vault-status.md`.
37
36
 
38
37
  ## CLI Tool Reference
39
38
 
40
- The stable portable path is the project-resolved CLI launcher. In an initialized project, prefer `node .agents/myco-cli.cjs` because it reads `.myco/runtime.command` in project scope and therefore works with dogfood aliases, worktree-local runtimes, and renamed binaries. The sibling `.agents/myco-run.cjs` launcher is reserved for capture hooks and may intentionally route git worktrees through the main checkout runtime so session data lands in the main vault. If the CLI launcher is not present, use host MCP tools when available, then fall back to `myco-run` or `myco` only when the command is known to be on PATH for this project.
39
+ The stable portable path is the `myco` CLI on your PATH. Prefer `myco tool call …`: the binary walks up from the working directory for a `.myco/runtime.command` pin before dispatching, so it automatically honors dogfood aliases, worktree-local runtimes, and renamed binaries. (The project-local `.agents/myco-cli.cjs` launcher that earlier versions shipped is retired — the global install no longer writes it.) When `myco` is not on PATH — e.g. GUI- or launchd-spawned agents whose environment omits `~/.local/bin` — fall back to the absolute global launcher the hooks themselves use: `node ~/.myco/launcher.cjs tool call …`, which performs the same layered pin resolution. Host MCP tools (`myco_*`) are the other fallback when the agent exposes Myco cleanly.
41
40
 
42
- Project-resolved CLI:
41
+ Myco CLI:
43
42
 
44
43
  ```bash
45
- node .agents/myco-cli.cjs tool list --json
46
- node .agents/myco-cli.cjs tool call <tool-name> --json --input '<json>'
47
- node .agents/myco-cli.cjs tool call <tool-name> --json --input @payload.json
44
+ myco tool list --json
45
+ myco tool call <tool-name> --json --input '<json>'
46
+ myco tool call <tool-name> --json --input @payload.json
48
47
  ```
49
48
 
50
49
  **Use `--input @file.json` whenever the payload contains backticks, code fences, multi-line strings, or markdown.** Agent shells often re-wrap commands through an outer `eval`, and backticks inside the inner single-quoted JSON get command-substituted before the CLI sees them — what you intended as literal `` `foo.ts` `` in spore content becomes the shell trying to execute `foo.ts`. The `@file` form sidesteps this entirely because the JSON never travels through shell escape resolution. Reserve the inline form for short single-line payloads with no special characters (e.g. `{"op":"get","id":"..."}`).
@@ -54,7 +53,7 @@ node .agents/myco-cli.cjs tool call <tool-name> --json --input @payload.json
54
53
  cat > /tmp/payload.json <<'EOF'
55
54
  { "op": "save", "type": "gotcha", "content": "Use `npm test`, not `bun test <subset>`..." }
56
55
  EOF
57
- node .agents/myco-cli.cjs tool call myco_spores --json --input @/tmp/payload.json
56
+ myco tool call myco_spores --json --input @/tmp/payload.json
58
57
  ```
59
58
 
60
59
  If the CLI is genuinely unavailable or both inline and `@file` forms fail repeatedly for the same payload, the host's MCP tool call (when Myco MCP is loaded — look for `myco_*` or `mcp__*myco*` entries in the available-tools list) is the fallback. Don't reach for MCP first — the CLI is the deliberate primary path; this skill is written around it.
@@ -63,26 +62,7 @@ Successful calls return `{ "ok": true, "tool": "<name>", "result": ... }`; failu
63
62
 
64
63
  The local Myco tool surface registers 7 core tools. When the project is connected to a Myco Collective, 4 additional `collective_*` tools are also available. Tools are defined in `packages/myco/src/tools/definitions.ts` — that file is the source of truth. MCP registers the same names when available.
65
64
 
66
- Use direct SQLite reads only as an expert, read-only fallback for complex analysis that cannot be answered through the project-resolved CLI or MCP.
67
-
68
- ## Myco Development Worktrees
69
-
70
- When developing Myco itself inside a git worktree, do not run `make dev-link`. That target rewrites shared `~/.local/bin/myco-*` symlinks and can redirect other active agents to the worktree binary.
71
-
72
- Use the worktree-scoped pattern instead:
73
-
74
- ```bash
75
- make dev-link-worktree
76
- ```
77
-
78
- This builds the worktree binary and writes the worktree's `.myco/runtime.command` directly to `packages/myco-<target>/bin/myco`. That file is local runtime state and is not inherited when a worktree is created, so run the command from each worktree that needs project-scoped CLI/tool testing.
79
-
80
- Runtime scopes stay separate:
81
-
82
- - `.agents/myco-run.cjs` is the capture launcher for hooks; in git worktrees it can resolve through the main checkout runtime so session capture stays attached to the main vault.
83
- - `.agents/myco-cli.cjs` is the project launcher for CLI/tool calls; in git worktrees it prefers the worktree-local `.myco/runtime.command`, then falls back to the main checkout pin.
84
-
85
- Remove only the worktree pin with `make dev-unlink-worktree`. Use `make dev-unlink` only when intentionally removing the shared dev symlinks from the main checkout.
65
+ Use direct SQLite reads only as an expert, read-only fallback for complex analysis that cannot be answered through the `myco` CLI or MCP.
86
66
 
87
67
  ### myco_cortex — Get Cortex intelligence
88
68
 
@@ -95,7 +75,7 @@ Retrieve Cortex-produced project intelligence: the pre-computed project digest,
95
75
  CLI:
96
76
 
97
77
  ```bash
98
- node .agents/myco-cli.cjs tool call myco_cortex --json --input '{"op":"digest","tier":5000}'
78
+ myco tool call myco_cortex --json --input '{"op":"digest","tier":5000}'
99
79
  ```
100
80
 
101
81
  Tiers: `1500` (executive briefing), `5000` (default), `10000` (comprehensive). Prefer this over `myco_search` for broad project orientation; use `myco_search` when you need specific prior decisions or bug fixes.
@@ -103,9 +83,17 @@ Tiers: `1500` (executive briefing), `5000` (default), `10000` (comprehensive). P
103
83
  Canopy map:
104
84
 
105
85
  ```bash
106
- node .agents/myco-cli.cjs tool call myco_cortex --json --input '{"op":"canopy_map"}'
86
+ myco tool call myco_cortex --json --input '{"op":"canopy_map"}'
87
+ ```
88
+
89
+ Current generated instructions:
90
+
91
+ ```bash
92
+ myco tool call myco_cortex --json --input '{"op":"instructions"}'
107
93
  ```
108
94
 
95
+ When delegating work, include the returned instructions verbatim in the delegated prompt alongside the task-specific instructions. Do not assume the returned instructions have a particular heading or section name; they are generated project guidance and may change over time.
96
+
109
97
  Canopy entry returned by search:
110
98
 
111
99
  ```json
@@ -123,7 +111,7 @@ Search across sessions, plans, spores, skills, and Canopy file summaries.
123
111
  CLI:
124
112
 
125
113
  ```bash
126
- node .agents/myco-cli.cjs tool call myco_search --json --input '{"query":"why did we choose JWT over session cookies","type":"spore","limit":5}'
114
+ myco tool call myco_search --json --input '{"query":"why did we choose JWT over session cookies","type":"spore","limit":5}'
127
115
  ```
128
116
 
129
117
  **When to use**: searching for prior decisions, debugging context, understanding rationale, or finding source files by what they do. The `type` filter narrows results — use `"spore"` for decisions/gotchas, `"session"` for session history, `"plan"` for plans, `"skill"` for skills, `"canopy"` for file summaries, or omit for all. Each result includes a stable `id` and, when the entity is retrievable, a `retrieve` object with the exact tool input to fetch it.
@@ -165,6 +153,8 @@ Session association is derived by the daemon; the MCP client does not pass it.
165
153
 
166
154
  List plans, retrieve a single plan's full content by ID, save a plan, or delete one.
167
155
 
156
+ Before creating a new plan or spec, or when existing plans may already cover the work, list plans and read any relevant ones before drafting something new. You do not need to run a plan lookup before every small implementation edit.
157
+
168
158
  ```json
169
159
  { "op": "list", "status": "active" }
170
160
  ```
@@ -306,7 +296,7 @@ The vault should get sharper over time, not just bigger. Every session should le
306
296
 
307
297
  1. `myco_cortex` op `"canopy_map"` for project layout, then `myco_search` with your branch and key files
308
298
  2. `myco_sessions` filtered by branch to see prior session summaries
309
- 3. `myco_plans` to check if there's an active plan
299
+ 3. If you are planning new work or the task may overlap existing specs, use `myco_plans` to check for active plans
310
300
  4. `myco_plans` op `"save"` after generating or revising a plan that should persist in Myco
311
301
 
312
302
  ### After fixing a tricky bug
@@ -323,26 +313,26 @@ The vault should get sharper over time, not just bigger. Every session should le
323
313
 
324
314
  ## Reconfiguration
325
315
 
326
- To change LLM providers, models, or digest settings on an existing vault, see `references/reconfiguration.md`. It covers the exact CLI commands, flag names, and order of operations (setup-llm → restart → rebuild if needed → verify).
316
+ To change embedding settings or Cortex injection behavior on an existing vault, see `references/reconfiguration.md`. It covers the current CLI commands, flag names, and order of operations (setup-llm → restart → rebuild if needed → verify).
327
317
 
328
318
  ## Maintenance
329
319
 
330
320
  For the full CLI reference with all flags, see `references/cli-usage.md`.
331
321
 
332
- All CLI commands use `node` with the CLI script inside the plugin root. Run commands as:
322
+ Prefer the `myco` CLI from the initialized project root:
333
323
 
334
324
  ```
335
- node <plugin-root>/dist/src/cli.js <command> [args]
325
+ myco <command> [args]
336
326
  ```
337
327
 
338
- Where `<plugin-root>` is the agent's plugin root environment variable (e.g., the value of `CLAUDE_PLUGIN_ROOT` or `CURSOR_PLUGIN_ROOT`).
328
+ The binary honors project and worktree runtime pins — it walks up from the working directory for `.myco/runtime.command`. When `myco` is not on PATH, use the absolute global launcher `node ~/.myco/launcher.cjs <command> [args]`, which resolves the same pins.
339
329
 
340
330
  ### Reprocessing sessions
341
331
 
342
332
  If observations were lost due to a bug, or if you want to re-extract observations with a different LLM, run the `reprocess` command:
343
333
 
344
334
  ```
345
- node <plugin-root>/dist/src/cli.js reprocess
335
+ myco reprocess
346
336
  ```
347
337
 
348
338
  This re-reads all session transcripts, re-extracts observations, and re-indexes everything. Existing spores are preserved — new observations are additive.
@@ -354,9 +344,9 @@ Options:
354
344
  ### Digest management
355
345
 
356
346
  ```
357
- node <plugin-root>/dist/src/cli.js digest # Run incremental digest cycle
358
- node <plugin-root>/dist/src/cli.js digest --tier 3000 # Reprocess a specific tier (clean slate)
359
- node <plugin-root>/dist/src/cli.js digest --full # Reprocess all tiers from scratch
347
+ myco digest # Run incremental digest cycle
348
+ myco digest --tier 3000 # Reprocess a specific tier (clean slate)
349
+ myco digest --full # Reprocess all tiers from scratch
360
350
  ```
361
351
 
362
352
  ### Vault intelligence
@@ -364,8 +354,8 @@ node <plugin-root>/dist/src/cli.js digest --full # Reprocess all tiers fro
364
354
  Supersession happens automatically on every spore write. For vault-wide cleanup, see `references/cli-usage.md` for full flags:
365
355
 
366
356
  ```
367
- node <plugin-root>/dist/src/cli.js agent # Run the intelligence agent
368
- node <plugin-root>/dist/src/cli.js agent --dry-run # Preview without writing
357
+ myco agent # Run the intelligence agent
358
+ myco agent --dry-run # Preview without writing
369
359
  ```
370
360
 
371
361
  For patterns on when to manually supersede or consolidate, see `references/wisdom.md`.
@@ -373,10 +363,10 @@ For patterns on when to manually supersede or consolidate, see `references/wisdo
373
363
  ### Other maintenance commands
374
364
 
375
365
  ```
376
- node <plugin-root>/dist/src/cli.js version # Check plugin version
377
- node <plugin-root>/dist/src/cli.js rebuild # Re-index all records
378
- node <plugin-root>/dist/src/cli.js stats # Check vault health
379
- node <plugin-root>/dist/src/cli.js verify # Test provider connectivity
380
- node <plugin-root>/dist/src/cli.js config get intelligence.llm.model
381
- node <plugin-root>/dist/src/cli.js config set intelligence.llm.model phi4
366
+ myco version # Check plugin version
367
+ myco rebuild # Re-index all records
368
+ myco stats # Check vault health
369
+ myco verify # Test embedding/provider connectivity
370
+ myco setup-llm --show
371
+ myco setup-llm --embedding-provider ollama --embedding-model bge-m3
382
372
  ```
package/skills/myco/references/cli-usage.md CHANGED
@@ -1,10 +1,10 @@
1
1
  # Myco CLI Reference
2
2
 
3
- All CLI commands are invoked as:
3
+ In an initialized project, prefer the `myco` CLI:
4
4
 
5
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js <command> [flags]
5
+ myco <command> [flags]
6
6
 
7
- Where `${CLAUDE_PLUGIN_ROOT}` resolves to the plugin root directory (set by the agent automatically).
7
+ It honors project and worktree runtime pins — the binary walks up from the working directory for `.myco/runtime.command`. When `myco` is not on PATH (e.g. GUI- or launchd-spawned agents), use the absolute global launcher `node ~/.myco/launcher.cjs <command> [flags]`, which resolves the same pins.
8
8
 
9
9
  ---
10
10
 
@@ -16,42 +16,30 @@ Initializes a new Myco vault. Skipped automatically if the vault is already init
16
16
 
17
17
  | Flag | Type | Description |
18
18
  |------|------|-------------|
19
- | `--vault <path>` | string | Custom vault directory (supports `~/` expansion) |
20
- | `--llm-provider <name>` | string | `ollama`, `lm-studio`, or `anthropic` |
21
- | `--llm-model <name>` | string | Model name |
22
- | `--llm-url <url>` | string | Provider base URL |
23
- | `--embedding-provider <name>` | string | `ollama` or `lm-studio` |
19
+ | `--project <path>` | string | Project root to initialize |
20
+ | `--grove <name\|id>` | string | Grove to bind this project to |
21
+ | `--worktree` | boolean | Bootstrap hook files in a git worktree |
22
+ | `--non-interactive` | boolean | Run without prompts |
23
+ | `--embedding-provider <name>` | string | Embedding provider for new vaults |
24
24
  | `--embedding-model <name>` | string | Embedding model name |
25
25
  | `--embedding-url <url>` | string | Embedding provider base URL |
26
- | `--user <name>` | string | Username for team-enabled vault |
27
- | `--team` | boolean | Enable team collaboration mode |
28
- | `--tiers <csv>` | string | Comma-separated digest tier list (e.g., `1500,3000,5000`) |
29
- | `--inject-tier <number>` | number | Tier to auto-inject at session start |
30
- | `--context-window <number>` | number | Context window size for digest operations |
31
26
 
32
27
  **Example:**
33
28
 
34
29
  ```sh
35
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js init \
36
- --llm-provider ollama \
37
- --llm-model qwen2.5-coder:14b \
30
+ myco init \
38
31
  --embedding-provider ollama \
39
32
  --embedding-model bge-m3
40
33
  ```
41
34
 
42
35
  ---
43
36
 
44
- ### `setup-llm` — Change LLM and embedding provider settings
37
+ ### `setup-llm` — Change embedding provider settings
45
38
 
46
- Reconfigures intelligence backend without reinitializing the vault.
39
+ Reconfigures Grove-tier embedding settings without reinitializing the vault. LLM configuration is managed by the Myco agent harness; `setup-llm` ignores legacy `--llm-*` flags.
47
40
 
48
41
  | Flag | Type | Description |
49
42
  |------|------|-------------|
50
- | `--llm-provider <name>` | string | Provider name (`ollama`, `lm-studio`, `anthropic`) |
51
- | `--llm-model <name>` | string | Model name |
52
- | `--llm-url <url>` | string | Provider base URL |
53
- | `--llm-context-window <number>` | number | Context window in tokens |
54
- | `--llm-max-tokens <number>` | number | Max output tokens |
55
43
  | `--embedding-provider <name>` | string | Embedding provider name |
56
44
  | `--embedding-model <name>` | string | Embedding model name |
57
45
  | `--embedding-url <url>` | string | Embedding base URL |
@@ -63,52 +51,19 @@ Note: changing the embedding model requires running `rebuild` afterward to re-em
63
51
 
64
52
  ```sh
65
53
  # Show current settings
66
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js setup-llm --show
54
+ myco setup-llm --show
67
55
 
68
- # Switch to Anthropic
69
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js setup-llm \
70
- --llm-provider anthropic \
71
- --llm-model claude-opus-4-5
56
+ # Change embedding model
57
+ myco setup-llm \
58
+ --embedding-provider ollama \
59
+ --embedding-model bge-m3
72
60
  ```
73
61
 
74
62
  ---
75
63
 
76
- ### `setup-digest` — Configure digest and capture settings
77
-
78
- Controls the continuous reasoning system: metabolism timing, tier configuration, and per-operation token budgets.
64
+ ### `setup-digest` — Deprecated
79
65
 
80
- | Flag | Type | Description |
81
- |------|------|-------------|
82
- | `--enabled <true\|false>` | boolean | Enable or disable digest |
83
- | `--tiers <csv>` | string | Comma-separated token tier list |
84
- | `--inject-tier <number\|null>` | number\|null | Auto-inject tier at session start (`null` to disable) |
85
- | `--provider <name\|null>` | string\|null | Digest-specific provider (`null` = inherit from main LLM) |
86
- | `--model <name\|null>` | string\|null | Digest-specific model (`null` = inherit) |
87
- | `--base-url <url\|null>` | string\|null | Digest provider base URL (`null` = inherit) |
88
- | `--context-window <number>` | number | Context window for digest |
89
- | `--keep-alive <duration>` | string | Keep model loaded (Ollama only, e.g., `30m`) |
90
- | `--gpu-kv-cache <true\|false>` | boolean | GPU KV cache offload (LM Studio only) |
91
- | `--active-interval <seconds>` | number | Metabolism active processing interval |
92
- | `--dormancy-threshold <seconds>` | number | Time before entering dormancy |
93
- | `--max-notes <number>` | number | Max substrate notes per digest cycle |
94
- | `--extraction-tokens <number>` | number | Max tokens for spore extraction |
95
- | `--summary-tokens <number>` | number | Max tokens for session summaries |
96
- | `--title-tokens <number>` | number | Max tokens for session titles |
97
- | `--classification-tokens <number>` | number | Max tokens for artifact classification |
98
- | `--show` | boolean | Display current settings and exit |
99
-
100
- **Example:**
101
-
102
- ```sh
103
- # Show current digest config
104
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js setup-digest --show
105
-
106
- # Use a faster model just for digest, with shorter active interval
107
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js setup-digest \
108
- --model qwen2.5:7b \
109
- --active-interval 120 \
110
- --dormancy-threshold 600
111
- ```
66
+ Digest and Cortex configuration now live in the normal scoped config/UI surfaces. `setup-digest` prints a deprecation message and points users back to `setup-llm` for embedding settings.
112
67
 
113
68
  ---
114
69
 
@@ -120,16 +75,16 @@ Direct access to vault config via dot-path notation. Values are parsed as JSON f
120
75
 
121
76
  ```sh
122
77
  # Read a value
123
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js config get intelligence.llm.model
78
+ myco config get cortex.instructions.inject_on_session_start
124
79
 
125
80
  # Write a value
126
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js config set intelligence.llm.model qwen2.5-coder:14b
81
+ myco config set cortex.instructions.inject_on_session_start true
127
82
 
128
83
  # Write a non-string value (parsed as JSON)
129
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js config set digest.enabled true
84
+ myco config set cortex.spores.max_per_prompt 3
130
85
  ```
131
86
 
132
- Restart the daemon after changes: `node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js restart`
87
+ Restart the daemon after changes that affect runtime behavior: `myco restart`
133
88
 
134
89
  ---
135
90
 
@@ -155,12 +110,12 @@ Output is JSON:
155
110
 
156
111
  ### `verify` — Test LLM and embedding connectivity
157
112
 
158
- Sends a test prompt to the LLM and a test embed to the embedding provider. Exits 0 if both pass, 1 if either fails.
113
+ Sends a test embed to the configured embedding provider. Exits 0 if it passes, 1 if it fails. LLM configuration is managed by the Myco agent harness.
159
114
 
160
115
  No flags.
161
116
 
162
117
  ```sh
163
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js verify
118
+ myco verify
164
119
  ```
165
120
 
166
121
  ---
@@ -172,7 +127,7 @@ Shows session/spore/plan counts, spore type breakdown, vector count, and daemon
172
127
  No flags.
173
128
 
174
129
  ```sh
175
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js stats
130
+ myco stats
176
131
  ```
177
132
 
178
133
  Typical output:
@@ -205,13 +160,13 @@ Components: `processor`, `embeddings`, `hooks`, `lifecycle`, `daemon`, `lineage`
205
160
 
206
161
  ```sh
207
162
  # Show last 20 lines
208
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js logs -n 20
163
+ myco logs -n 20
209
164
 
210
165
  # Follow errors from the processor
211
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js logs -f -l error -c processor
166
+ myco logs -f -l error -c processor
212
167
 
213
168
  # Show logs from a specific window
214
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js logs \
169
+ myco logs \
215
170
  --since 2025-01-01T10:00:00Z \
216
171
  --until 2025-01-01T11:00:00Z
217
172
  ```
@@ -225,7 +180,7 @@ node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js logs \
225
180
  Runs semantic search (primary) with FTS fallback across sessions, spores, and plans.
226
181
 
227
182
  ```sh
228
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js search "why did we choose sqlite over postgres"
183
+ myco search "why did we choose sqlite over postgres"
229
184
  ```
230
185
 
231
186
  ---
@@ -235,7 +190,7 @@ node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js search "why did we choose sqlite over
235
190
  Shows all results with similarity scores and no threshold filtering. Useful for tuning embedding thresholds.
236
191
 
237
192
  ```sh
238
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js vectors "session lifecycle hooks"
193
+ myco vectors "session lifecycle hooks"
239
194
  ```
240
195
 
241
196
  ---
@@ -249,10 +204,10 @@ node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js vectors "session lifecycle hooks"
249
204
 
250
205
  ```sh
251
206
  # Show latest session
252
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js session
207
+ myco session
253
208
 
254
209
  # Show a specific session by partial ID
255
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js session ac5220
210
+ myco session ac5220
256
211
  ```
257
212
 
258
213
  ---
@@ -266,7 +221,7 @@ Sends SIGTERM to the running daemon, waits for it to exit, and spawns a fresh in
266
221
  No flags.
267
222
 
268
223
  ```sh
269
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js restart
224
+ myco restart
270
225
  ```
271
226
 
272
227
  Run this after any daemon code changes to pick up new behavior.
@@ -280,7 +235,7 @@ Re-indexes all records. Superseded and archived spores are skipped.
280
235
  No flags.
281
236
 
282
237
  ```sh
283
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js rebuild
238
+ myco rebuild
284
239
  ```
285
240
 
286
241
  Run this after changing the embedding model (via `setup-llm`) to regenerate all embeddings with the new model.
@@ -302,13 +257,13 @@ When `--tier` or `--full` is used, the cycle reads all records (ignoring the las
302
257
 
303
258
  ```sh
304
259
  # Run an incremental cycle (same as what the metabolism timer does)
305
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js digest
260
+ myco digest
306
261
 
307
262
  # Reprocess tier 3000 from scratch
308
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js digest --tier 3000
263
+ myco digest --tier 3000
309
264
 
310
265
  # Full rebuild of all tiers
311
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js digest --full
266
+ myco digest --full
312
267
  ```
313
268
 
314
269
  ---
@@ -327,10 +282,10 @@ Runs the intelligence agent to process unprocessed session data, extract observa
327
282
 
328
283
  ```sh
329
284
  # Run the default intelligence task
330
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js agent
285
+ myco agent
331
286
 
332
287
  # Preview what would be changed
333
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js agent --dry-run
288
+ myco agent --dry-run
334
289
  ```
335
290
 
336
291
  Note: `--dry-run` still runs LLM calls (to evaluate) — it just skips the writes. Use it to review before running on a vault for the first time.
@@ -350,13 +305,13 @@ Re-reads session transcripts, re-extracts observations with the current LLM, and
350
305
 
351
306
  ```sh
352
307
  # Reprocess all sessions
353
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js reprocess
308
+ myco reprocess
354
309
 
355
310
  # Reprocess one session
356
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js reprocess --session ac5220
311
+ myco reprocess --session ac5220
357
312
 
358
313
  # Re-index without re-extracting
359
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js reprocess --index-only
314
+ myco reprocess --index-only
360
315
  ```
361
316
 
362
317
  ---
@@ -366,7 +321,7 @@ node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js reprocess --index-only
366
321
  ### `version` — Show plugin version
367
322
 
368
323
  ```sh
369
- node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js version
324
+ myco version
370
325
  ```
371
326
 
372
327
  Also available as `--version` or `-v`.