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docs: add deployment modes documentation and update plans

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Add DEPLOYMENT-MODES.md with canonical mode taxonomy. Update CLI.md,
DEVELOPING.md, PRODUCT.md, and SPEC-implementation.md with local_trusted/
authenticated nomenclature. Revise humans-and-permissions plan with Better
Auth choice, bootstrap flow, unified invite semantics, and expanded criteria.
Add implementation guide and additional plan documents for cursor cloud
adapter and deployment auth mode consolidation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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doc/CLI.md
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@ -25,6 +25,18 @@ Choose local instance:
pnpm paperclip run --instance dev
```
## Deployment Modes
Mode taxonomy and design intent are documented in `doc/DEPLOYMENT-MODES.md`.
Current CLI behavior:
- `paperclip onboard` and `paperclip configure --section server` set deployment mode in config
- runtime can override mode with `PAPERCLIP_DEPLOYMENT_MODE`
- `paperclip run` and `paperclip doctor` do not yet expose a direct `--mode` flag
Target behavior (planned) is documented in `doc/DEPLOYMENT-MODES.md` section 5.
All client commands support:
- `--api-base <url>`