docs(SPEC-20): Update cloud-cli.md for project-scoped sync

Complete rewrite to reflect SPEC-20 architecture:
- Removed outdated mount/bisync workflow confusion
- Added clear problem/solution explanations
- Documented project-scoped sync model
- Explained what happens under the covers for each command
- Added use case examples with concrete scenarios
- Updated all commands to project-scoped approach
- Removed references to deprecated features
- Added troubleshooting with explanations

Documentation now ready for user testing.

Signed-off-by: phernandez <paul@basicmachines.co>

Author: phernandez