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chemenu/instructions/bootstrap.md
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feat!: installation only from a release, into an empty folder; upstream merge/verify and private-instance.md removed, dist adopt, shell-neutral instructions (#153)
Files changed:
- .gitea/workflows/ci.yml
- .gitea/workflows/release.yml
- AGENTS.md
- CHANGES.md
- DEVELOPMENT.md
- EVALS.md
- INSTALL.md
- README.md
- VERSION
- docs/ownership-and-templates.md
- instructions/CONTRACT.md
- instructions/bootstrap.md
- instructions/dev/dev-setup.md
- instructions/dev/stack-dev/SKILL.md
- instructions/gates.md
- instructions/ingest-large-tree.md
- instructions/kb-profiles.md
- instructions/mcp-read-server.md
- instructions/migrations/3.0.0-authoring-conventions.md
- instructions/preflight.md
- instructions/private-instance.md
- instructions/session-setup.md
- instructions/setup-instance.md
- instructions/upgrade-instance.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli.py
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/dist_cmd.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/git_publish.py
- tools/chemenu/commands/upstream_cmd.py
- tools/chemenu/commands/work_cmd.py
- tools/chemenu/config.py
- tools/chemenu/ownership.py
- tools/chemenu/tests/test_cli.py
- tools/chemenu/tests/test_dist_cmd.py
- tools/chemenu/tests/test_instructions_shell.py
- tools/chemenu/tests/test_preflight.py
- tools/chemenu/tests/test_preflight_pwsh.py
- tools/chemenu/tests/test_run_budget.py
- tools/chemenu/tests/test_upstream_cmd.py
- tools/chemenu/toc.py
- tools/preflight.ps1
- tools/preflight.sh
2026-10-01 22:12:09 +02:00

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Markdown

---
type: types/instruction.md
name: bootstrap
description: Prepare a fresh clone of an existing instance (a second machine, a new checkout) for work - run the preflight (tool paths and the tools venv) and publish the skills into the harness directories, which are generated and not committed.
---
# Bootstrap a fresh clone
An instance lives in its own git repository, so a second machine - or a new checkout on the same
one - gets it with `git clone`. What the clone does not carry is everything that describes one
machine rather than the instance: the tool paths and the tools venv, and the published skills.
`.agents/skills/` and `.claude/skills/` are generated copies of the skill directories under
`instructions/`, and both are gitignored. A fresh clone therefore has no skills at all until
they are published: the agent harness will not offer `wiki-ingest`, `wiki-query`,
`wiki-manage`, `wiki-lint`, `wiki-status` or `gtd-weekly-review` before this runs.
## When to run
- After cloning the instance's repository.
- After `instructions/<name>/SKILL.md` is added, renamed, or edited.
- Whenever `tools/wikitool instructions verify` reports a missing or drifted copy.
## Steps
1. **Run the preflight** (once per clone, and again after moving it) - see
[preflight.md](preflight.md). It records the tool paths in `.wikitool-tools.json` and
creates `tools/.venv`; until it exits 0, `tools/wikitool` refuses to start:
```bash
tools/preflight.sh
```
From PowerShell 7 on Windows, run the twin instead - same questions, same file:
```powershell
pwsh -NoProfile -ExecutionPolicy Bypass -File tools/preflight.ps1
```
On exit 42, show its output to the user verbatim and wait.
2. **Publish the skills:**
```bash
tools/wikitool instructions sync
```
3. **Verify:**
```bash
tools/wikitool instructions verify
```
Expected: `OK`. If it reports drift, re-run `sync` - the source under `instructions/` always
wins, and a copy is never edited directly.
4. **Check for personalization.** A clone predating the personalization files has no
`USER.md`/`SOUL.md`, and `tools/wikitool doctor` reports `personalization: FAIL` for it.
That is a one-off catch-up, not a bootstrap step that repeats: run **only** the
personalization step (5) of [setup-instance.md](setup-instance.md), not the whole
procedure - this clone already has its git repo, author identity and content. A clone that
already carries both files needs nothing here.
5. **Offer to record the environment.** `ENVIRONMENT.md` is gitignored, so a fresh clone never
has one, and every session in it re-asks which harness is in use, which MCP servers are
reachable, and which remote `publish` talks to. Copy `ENVIRONMENT.md.template` to
`ENVIRONMENT.md`, fill in what is already known from this clone (`git remote -v`, the
harness you are running in, `tools/wikitool instructions list`), ask the user for the rest,
and drop the `wikitool:template-unfilled` line.
**Optional, and it stays optional.** Skip it and everything still works - `doctor` reports
`environment: absent (optional)`, not a failure. Skip it *silently*, though, and the next
session pays for it again. Never guess an entry: a wrong remote or an MCP server that is not
there is worse than the empty section it replaced, because it gets believed.
6. **Restart the agent session** if it was already running. Harnesses read the skill
directories at startup, so skills published mid-session are not picked up.
7. **Expect a lingering `session-id` WARN.** A `tools/wikitool doctor` run at this point reports
`OK` throughout except `session-id: WARN` - that check is scoped to the working session, not
the clone, so a freshly bootstrapped checkout with no `WIKITOOL_SESSION_ID` exported yet
always shows it. This is expected, not a Bootstrap gap: exporting it here would only be true
for this one-off setup run, not for whichever session picks up the actual work next, in a new
shell after step 6's restart. Run [session-setup.md](session-setup.md) at the start of that
session instead.
## Scope
This does not apply to anything under `kb/`, `raw/` or `reports/`; those are committed and
present immediately after a clone. If the wiki content looks wrong after cloning, that is a
lint question, not a bootstrap one.
This also does not apply to a new instance installed from a release - it has no git history, no
author identity, and no generated indexes yet. That is [setup-instance.md](setup-instance.md), a
longer procedure this one is a single step of.