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

instructions/bootstrap.md

@@ -1,11 +1,15 @@
 ---
 type: types/instruction.md
 name: bootstrap
-description: Prepare a fresh clone 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.
+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`,
@@ -13,7 +17,7 @@ they are published: the agent harness will not offer `wiki-ingest`, `wiki-query`
 
 ## When to run
 
-- After cloning the repository.
+- 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.
 
@@ -53,7 +57,7 @@ they are published: the agent harness will not offer `wiki-ingest`, `wiki-query`
 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 (6) of [setup-instance.md](setup-instance.md), not the whole
+   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.
 
@@ -86,6 +90,6 @@ This does not apply to anything under `kb/`, `raw/` or `reports/`; those are com
 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 fresh instance created via `tools/wikitool dist export` - 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.
+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.