# Debug Mycelium

> Use when mycelium sync fails, items not appearing in tools, enable/disable not working, MCP not connecting, config conflicts between levels, EACCES permission errors, or any unexpected mycelium CLI behavior.

- **Type:** Skill
- **Install:** `agentstack add skill-bytemines-mycelium-debug-mycelium`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [bytemines](https://agentstack.voostack.com/s/bytemines)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [bytemines](https://github.com/bytemines)
- **Source:** https://github.com/bytemines/mycelium/tree/main/.claude/skills/debug-mycelium
- **Website:** https://mycelium.to

## Install

```sh
agentstack add skill-bytemines-mycelium-debug-mycelium
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Debug Mycelium

Systematic diagnostic workflow using Mycelium's built-in SQLite trace database. Traces capture 16 dimensions per operation — filter to the exact slice that matters, never read the full DB.

## When to Use

- `mycelium sync` fails or skips items
- Item shows as enabled but doesn't appear in tool config
- Enable/disable has no effect
- MCP server not connecting after sync
- Config conflicts between global/machine/project levels
- Permission errors (EACCES, EPERM)
- Migration imports wrong or missing items
- "It worked before but stopped" scenarios

## Step 1: Gather Context

Ask the user:
- What command were you running? (sync, enable, disable, add, remove, migrate)
- What item is affected? (MCP name, skill name, plugin name)
- Which tool? (cursor, claude-code, vscode, etc.)
- What did you expect vs what happened?

## Step 2: Pull Filtered Traces

Run the `mycelium report` command with appropriate filters. Always start narrow:

```bash
# If user mentions a specific item:
mycelium report --item  --since 1h --format table

# If user mentions a specific tool:
mycelium report --tool  --level error,warn --since 1h --format table

# If user mentions a specific command:
mycelium report --cmd  --since 1h --format table

# For full context (JSONL for analysis):
mycelium report --item  --full --format jsonl
```

**Important**: Always use `--since` to limit results. Never pull the full DB.

## Step 3: Check Health

```bash
mycelium doctor --json
```

Look for:
- Failed config checks (broken YAML/JSON/TOML)
- Broken symlinks (skills not properly linked)
- Missing directories
- MCP connectivity failures

## Step 4: Check Manifest State

```bash
# Read the manifest directly
cat ~/.mycelium/global/manifest.yaml

# Or for project-level:
cat .mycelium/manifest.yaml
```

Look for:
- `state` field: is the item `enabled`, `disabled`, or `deleted`?
- `source` field: where did this item come from?
- Missing items: was the item never added?

## Step 5: Check Tool Config

Read the tool's native config file to verify the sync result:

| Tool | Config Path |
|------|------------|
| Claude Code | `~/.claude.json` or `.claude/settings.json` |
| Cursor | `~/.cursor/mcp.json` |
| VS Code | `~/.vscode/settings.json` |
| Codex | `~/.codex/config.toml` |
| Gemini CLI | `~/.gemini/settings.json` |
| OpenCode | `~/.opencode/config.json` |
| OpenClaw | `~/.openclaw/plugins.json` |

Verify the MCP entry exists and has correct structure for that tool's format.

## Step 6: Analyze the Trace

Read the JSONL output from Step 2. Look for these patterns:

### Common Issues

**Item not syncing (state bug)**:
- Check trace for `op: "filter"` entries — was the item filtered out?
- Check `state` dimension — is it `disabled` or `deleted`?
- Check `source` — was it from a plugin that got removed?

**Permission errors**:
- Check trace for `error` containing "EACCES" or "EPERM"
- Check `path` dimension — which file had the permission issue?
- Fix: `chmod` the file or run with appropriate permissions

**Config parse errors**:
- Check trace for `format` dimension — which format failed?
- Check `path` — which config file is malformed?
- Validate the file manually: `cat  | python3 -m json.tool`

**Adapter method fallback**:
- Check `method` dimension — did it try "cli" then fall back to "file"?
- Check if the tool's CLI is installed and accessible

**Merge conflicts**:
- Check trace for `configLevel` — which level caused the conflict?
- Check `phase: "merge"` entries for warnings
- Read all 3 config levels: global, machine, project

**MCP still in tool config after disable**:
- `mycelium disable ` updates manifest but MCP remains in `~/.claude.json` (or other tool configs)
- Root cause: item was registered in wrong manifest section (e.g. `skills.massive` instead of `mcps.massive`)
- Check manifest: `cat ~/.mycelium/manifest.yaml` — verify item is in `mcps:` section, not `skills:`
- Fix: move the entry to the correct section, then run `mycelium disable ` again
- After fix, disable now calls `adapter.remove()` on tool configs and enable calls `adapter.add()`

**Item not found (typo)**:
- Check `item` dimension — does the name have a typo? (e.g., `postgress-mcp` vs `postgres-mcp`)
- Query with LIKE: `mycelium report --item postgres` to find all variants
- Compare against manifest to find the correct name

## Step 7: Generate Report

Once you've identified the issue, create a structured report:

```markdown
## Problem
[1-2 sentence summary of what's broken]

## Root Cause
[What the trace analysis revealed]

## Relevant Trace
\`\`\`
[Paste the key 5-10 trace entries that show the problem]
\`\`\`

## Doctor Output
[Any relevant failed/warning checks]

## Manifest State
[Item state and source from manifest]

## Environment
- OS: [from mycelium report --full]
- Node: [version]
- Mycelium: [version]
- Tool: [affected tool and version]

## Fix
[Suggested fix — either a command to run or a code change to make]
```

## Step 8: Apply Fix or File Issue

If the fix is a user action (config change, permission fix):
- Guide the user through the fix
- Run `mycelium sync` to verify
- Run `mycelium report --item  --since 5m` to confirm no more errors

If the fix requires a code change:
- Save the report to a file: `mycelium report --item  --full --output /tmp/mycelium-report.jsonl`
- The user can paste the report into a GitHub issue
- Or create a PR directly with the fix

## Plugin Takeover Debugging

When plugin takeover isn't working (skills/agents/commands from Claude Code plugins not appearing or disappearing):

### Quick diagnosis

```bash
# All plugin operations
mycelium report --scope plugin --since 1h --format table

# Specific operation type (takeover, release, symlink-create, symlink-remove, health-check)
mycelium report --op takeover --since 1d --format table

# Symlink operations only
mycelium report --op symlink-create,symlink-remove --since 1h --format table

# Plugin health check results
mycelium report --op health-check --scope plugin --since 1h --format table

# All operations on a specific plugin
mycelium report --item superpowers@skillsmp --since 1d --format table
```

### Common plugin issues

**Component missing after disable/enable cycle**:
1. Check symlink operations: `mycelium report --op symlink-create,symlink-remove --since 1h`
2. Check if the component type is correct: look for `itemType` in trace entries (skill, agent, command)
3. Run doctor: `mycelium doctor` — check "Plugin Takeover" section for invariant violations
4. Fix: `mycelium sync` re-runs `syncPluginSymlinks()` to reconcile state

**Plugin shows as taken over but components aren't working**:
1. Check health: `mycelium doctor` — invariant checks verify symlinks, settings.json, cache
2. Check sync: `mycelium report --cmd plugin-sync --level error,warn`
3. Verify cache: `ls ~/.claude/plugins/cache///`

**Release didn't re-enable plugin**:
1. Check settings.json: `cat ~/.claude/settings.json | grep enabledPlugins`
2. Check traces: `mycelium report --op release --since 1h`
3. Check if all components were re-enabled: `mycelium report --scope manifest --item `

## Dashboard Debug Logging

For UI issues (sidebar flicker, toggle state, graph reloads), enable browser-side debug logging. Run in the browser console on `localhost:3378`:

```js
localStorage.setItem("mycelium:debug:panel", "1")  // [panel] animation lifecycle
localStorage.setItem("mycelium:debug:store", "1")  // [store] state operations
```

Refresh, reproduce the issue, then read `[panel]`/`[store]` logs in the console. Remove keys and refresh to disable.

## Dimension Reference

These are the filterable dimensions in `mycelium report`:

| Flag | Description | Values |
|------|------------|--------|
| `--cmd` | CLI command | sync, enable, disable, add, remove, migrate, doctor, plugin-sync, mcp |
| `--scope` | What type | mcp, skill, config, memory, hook, plugin, manifest |
| `--op` | Operation | takeover, release, symlink-create, symlink-remove, health-check, inject, sync, disable, enable |
| `--tool` | Which tool | claude-code, cursor, vscode, codex, gemini, opencode, openclaw, antigravity |
| `--item` | Item name | any MCP/skill/hook/plugin name |
| `--level` | Severity | debug, info, warn, error |
| `--state` | Manifest state | enabled, disabled, deleted |
| `--source` | Item source | plugin name or "manual" |
| `--trace` | Trace ID | sync-abc123 (from trace output) |
| `--project` | Project name | directory name |
| `--since` | Time range | 1h, 30m, 7d, 2026-02-10 |

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [bytemines](https://github.com/bytemines)
- **Source:** [bytemines/mycelium](https://github.com/bytemines/mycelium)
- **License:** MIT
- **Homepage:** https://mycelium.to

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-bytemines-mycelium-debug-mycelium
- Seller: https://agentstack.voostack.com/s/bytemines
- Browse the marketplace: https://agentstack.voostack.com/browse

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