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## Intent
Development choices (process, practices, architecture, backpressure) are
team-level decisions that belong in version control. Harness configuration
(autonomy profile, target agents, skills install) is developer/environment-level
and should be independently changeable without touching shared config files.
Previously everything was mixed into one `ade setup` wizard and persisted in
`config.yaml` / `config.lock.yaml`, making it impossible to adjust autonomy
without re-running the full setup flow.
## Key changes
- `ade setup` now only prompts for dev-choice facets (process, architecture,
practices, backpressure). Autonomy is excluded. Harness selection is gone.
Stages inline skill files to `.ade/skills/` (skipping locally modified ones),
then offers: "Would you like to configure your coding agent now?"
- New `ade configure` command (ephemeral — writes no config files):
1. Loads `config.lock.yaml` (requires setup to have run first)
2. Prompts for autonomy profile (rigid / sensible-defaults / max-autonomy / skip)
3. Prompts for harness selection
4. Installs to selected harnesses with the chosen permission policy merged in
5. Stages any new inline skills to `.ade/skills/` (skips modified ones), then
always installs all skills without a confirmation dialog
6. Prompts to initialise knowledge sources
- `ade install` outro now mentions `ade configure` so users know how to set
their autonomy profile after a fresh clone.
- README, CLI-design.md, and CLI-PRD.md updated to reflect the separation.
## Dependencies and side effects
- `config.yaml` and `config.lock.yaml` no longer contain `harnesses` or
`autonomy` keys — existing lock files with those keys remain readable
(`harnesses` is still used by `ade configure` as the default harness selection).
- All integration tests updated: setup calls no longer mock harness multiselect
or skills/knowledge confirmation prompts; `runConfigure` is mocked in setup tests.
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