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fix(setup): detect and respect existing .rtmx/ structure from init

rtmx setup hardcoded legacy docs/ paths, creating a divergent database
and requirements tree when run after rtmx init. Now detectProject()
checks for .rtmx/ artifacts first, and all phases use layout-aware
paths. Fresh projects default to the modern .rtmx/ layout.

Added REQ-E2E-005 with 5 E2E tests: init-then-setup coherence,
setup-alone defaults, existing-project preservation, legacy-mode
respect, and dogfood against the rtmx repo itself.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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