Migrate Doctor

What it does

When your agent uses it

• — upgrade.sh failed
• Bot wont start after upgrade
• Миграция сломалась
• Бот не стартует после обновления

Example prompts

• “t start after upgrade,”
• “/migrate-doctor”

Requirements

• Python 3
• A credential in TODOIST_API_KEY

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

1. 1Backup before any destructive step: tar czf ~/dbrain-backup-$(date +%s).tgz -C ~/projects agent-second-brain --exclude=.venv and note the…
2. 2Never modify or delete vault content (vault/daily, notes, cards). The vault is the user's data; migration touches code, units and runtime…
3. 3Prefer re-running bash upgrade.sh after each fix — it is idempotent. Fix the obstacle, not the symptom.
4. 4Typical obstacles and fixes
5. 5Report honestly: if a step failed, say so with the output. Never claim health you didn't verify.

What it can do on your machine

Read from SKILL.md and the folder at commit 7828ed6. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • git
  • claude
  • bash
  • uv

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md. Its commands use git and uv, which can reach the network depending on how they are called.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names these keys or tokens, usually read from environment variables:

  • TODOIST_API_KEY

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Migrate Doctor loads about 904 tokens when it runs. Until then it costs about 76 tokens; SKILL.md has 330 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~76

When it runs · the whole SKILL.md, loaded when a task matches

~904

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

• NoteMentions a .env fileSKILL.md:19

  brain-bot.service`, `TODOIST_API_KEY` in .env, mcp-config.json | Todoist/MCP era, `claude -p` per message |

• NoteRuns commands with sudoSKILL.md:28

  sudo systemctl list-units 'd-brain-*' --all      # legacy system-level

• NoteMentions a .env fileSKILL.md:32

  cat ~/projects/agent-second-brain/.env | grep -v 'TOKEN\|KEY'  # never print secrets

• NoteRuns commands with sudoSKILL.md:44

  - legacy system-level units conflict → `sudo systemctl disable --now 'd-brain-*'` and remove files from `/etc/systemd/s

• NoteMentions a .env fileSKILL.md:47

  ODOIST_API_KEY` / `DBRAIN_MODE` lines in .env → remove them (v3 ignores but they confuse humans)

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from smixs/agent-second-brain at commit 7828ed6, republished under its MIT licence (© smixs). 330 words, ~904 tokens.

name

migrate-doctor

description

Diagnose and repair a broken or non-standard agent-second-brain install/migration. Triggers — upgrade.sh failed, bot won't start after upgrade, "миграция сломалась", "бот не стартует после обновления", legacy d-brain units still present, brain session won't boot, doctor reports failures.

# What's installed and running?
systemctl --user list-units 'dbrain-*' --all
sudo systemctl list-units 'd-brain-*' --all      # legacy system-level
ls ~/.dbrain/ 2>/dev/null                         # runtime dir (v3)
tmux ls 2>/dev/null                               # brain sessions
git -C ~/projects/agent-second-brain log --oneline -3
cat ~/projects/agent-second-brain/.env | grep -v 'TOKEN\|KEY'  # never print secrets
claude auth status --json                         # needs "loggedIn": true
journalctl --user -u dbrain-bot -n 50 --no-pager

bash scripts/check-no-claude-p.sh                 # guard clean
systemctl --user is-active dbrain-bot dbrain-watchdog dbrain-process.timer dbrain-doctor.timer
uv run python -m d_brain.services.doctor          # ok=True
cat ~/.dbrain/STATUS.md                            # state: healthy

© smixs, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in vault/.claude/skills/migrate-doctor of smixs/agent-second-brain.

Open the folder on GitHubat commit 7828ed6