@goondocks/myco 0.27.17 → 0.27.19

package/skills/myco/references/vault-status.md

@@ -2,9 +2,9 @@
 
 This reference guides vault health assessment. Use it whenever you need to inspect the state of the Myco vault — whether debugging a problem, responding to a user's question about their vault, or running a routine check.
 
-**Primary data source:** `node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js stats`
+**Primary data source:** `node .agents/myco-cli.cjs stats`
 
-Supplement with `logs` for recent daemon activity and direct file checks for digest status.
+Supplement with `logs` for recent daemon activity and `myco_cortex` for Cortex/digest status.
 
 ---
 
@@ -13,7 +13,7 @@ Supplement with `logs` for recent daemon activity and direct file checks for dig
 Run the stats command to get a snapshot of vault state:
 
 ```sh
-node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js stats
+node .agents/myco-cli.cjs stats
 ```
 
 The output includes:
@@ -55,7 +55,7 @@ The daemon runs as a background HTTP process. Its state is persisted in `<vault>
 You can also restart it manually:
 
 ```sh
-node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js restart
+node .agents/myco-cli.cjs restart
 ```
 
 Do not treat a stopped daemon as a vault error — it is normal between sessions. The daemon starts on demand when a session begins.
@@ -64,57 +64,38 @@ Do not treat a stopped daemon as a vault error — it is normal between sessions
 
 ## Digest Status
 
-The digest system synthesizes vault knowledge into pre-computed context extracts. Check its state with direct file inspection.
+The digest system synthesizes vault knowledge into pre-computed context extracts served through Cortex.
 
 **Is digest enabled?**
 
-Read `digest.enabled` from `<vault>/myco.yaml`. If false or absent, skip digest checks.
+Read scoped Cortex config through the UI or config surface. The session-start toggles are under `cortex.instructions.*` and `cortex.digest.*`.
 
 **Which extracts exist?**
 
-List files in `<vault>/digest/`:
+Use `myco_cortex` to request the tier you care about:
 
-- `extract-1500.md` — ~1500 token tier
-- `extract-3000.md` — ~3000 token tier
-- `extract-5000.md` — ~5000 token tier
-- `extract-10000.md` — ~10000 token tier
-
-Report each file's size and last-modified timestamp. Missing tiers mean the digest has not yet run for that tier, or the tier is not configured.
-
-**Last digest cycle:**
-
-Read the last line of `<vault>/digest/trace.jsonl`. Each line is a JSON object with:
-
-- `cycleId` — short identifier for the cycle
-- `timestamp` — ISO timestamp of when the cycle ran
-- `tiersGenerated` — which tiers were written
-- `substrateCount` — number of records processed as input
-- `durationMs` — how long the cycle took
-
-**Metabolism config:**
-
-From `myco.yaml`, report:
+```sh
+node .agents/myco-cli.cjs tool call myco_cortex --json --input '{"op":"digest","tier":1500}'
+node .agents/myco-cli.cjs tool call myco_cortex --json --input '{"op":"digest","tier":5000}'
+```
 
-- Configured tiers (e.g., `[1500, 3000, 5000, 10000]`)
-- Inject tier — which tier is injected at session start
-- Context window size
-- Digest model — if `digest.intelligence.model` is set, report it; otherwise note "inherits from main LLM"
+Missing or not-ready responses mean the digest has not been generated for that tier yet or Cortex is disabled for the project.
 
 ---
 
 ## Intelligence Backend Health
 
-Test connectivity to the configured LLM and embedding providers:
+Test connectivity to the configured embedding provider:
 
 ```sh
-node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js verify
+node .agents/myco-cli.cjs verify
 ```
 
-This reports whether the LLM provider and embedding provider are reachable. If either is unreachable:
+This reports whether the embedding provider is reachable. The Myco agent LLM is managed by the agent harness. If embedding verification fails:
 
 - Check that the provider process is running (Ollama, LM Studio, etc.)
-- Review the model name in `myco.yaml` for typos
-- Re-run configuration with the appropriate CLI setup command
+- Review Grove-tier embedding settings with `node .agents/myco-cli.cjs setup-llm --show`
+- Re-run configuration with `setup-llm`
 
 ---
 
@@ -127,7 +108,7 @@ Check for these problems when assessing vault health:
 | **Stale buffers** | `.jsonl` files in `<vault>/buffer/` older than 24 hours | Events were captured but never processed — LLM may have been unavailable |
 | **Missing vault DB** | `<vault>/myco.db` does not exist | The vault database is missing or the project is not initialized; suggest `myco init` or check vault resolution |
 | **Missing vectors** | `<vault>/vectors.db` does not exist | Semantic search disabled; embeddings may be unconfigured |
-| **Old config version** | `version` in `myco.yaml` is less than `2` | Vault may need migration; suggest running `myco init` |
+| **Old config version** | `version` in `myco.yaml` is stale | Vault may need migration; suggest running `myco init` or `myco update` |
 
 Report all issues found, or "None found." if the vault is clean.
 
@@ -138,7 +119,7 @@ Report all issues found, or "None found." if the vault is clean.
 View recent daemon log output:
 
 ```sh
-node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js logs -n 20
+node .agents/myco-cli.cjs logs -n 20
 ```
 
 This shows the last 20 lines of daemon logs — useful for spotting errors, slow processing, or repeated failures.
@@ -217,8 +198,8 @@ Lineage tracks parent-child relationships between sessions. A high count of `sem
 
 | Issue | Action |
 |-------|--------|
-| Daemon not running | Will auto-start on next session; or run `node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js restart` |
+| Daemon not running | Will auto-start on next session; or run `node .agents/myco-cli.cjs restart` |
 | Stale buffers | Check if LLM provider was down during those sessions; events will process on next daemon start |
-| Missing index | Run `node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js rebuild` to regenerate FTS and vector indexes |
+| Missing index | Run `node .agents/myco-cli.cjs rebuild` to regenerate FTS and vector indexes |
 | Provider unreachable | Ensure the provider is running (e.g., `ollama serve`); verify model name in `myco.yaml`; reconfigure with CLI commands |
 | Config version < 2 | Run `myco init` to migrate the vault configuration |

package/skills/myco/references/wisdom.md

@@ -8,8 +8,8 @@ Myco automatically checks for supersession every time a new spore is written. Af
 
 For vault-wide cleanup (e.g., after a large refactor), use the CLI:
 ```sh
-node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js agent --dry-run  # preview
-node ${CLAUDE_PLUGIN_ROOT}/dist/src/cli.js agent             # execute
+node .agents/myco-cli.cjs agent --dry-run  # preview
+node .agents/myco-cli.cjs agent             # execute
 ```
 
 ## Supersede