fix: move conductor.json to repo root for proper detection (#88184)
## What?
Moves `conductor.json` from `.conductor/conductor.json` to the
repository root and updates script paths accordingly.
## Why?
Conductor searches for configuration files in a specific priority order:
1. Workspace root
2. Remote default branch
3. Repository root
The previous location at `.conductor/conductor.json` wasn't in the
standard search path, which could cause Conductor to not detect the
configuration properly. Moving to the repo root follows the [recommended
pattern from Conductor's
documentation](https://docs.conductor.build/core/conductor-json).
## How?
- Moved `conductor.json` to repository root
- Updated script paths from `./scripts/` to `./.conductor/scripts/`
- Scripts remain in `.conductor/scripts/` for organization