Repository Documentation Cleanup and Link Fixes

Review the repository documentation (README, docs/, inline guides). Remove content that is outdated or superseded, consolidate duplicated explanations into a single place, fix broken links, and make sure every document is reachable from the README. Deliver the changes as one pull request.

Docs cleanup merged (PR #75): dropped dangling "PRD D5" ref, replaced stale gate timing, consolidated duplicated gate/caching/dc-tier prose into pointers, linked tools/build.js from README. All md links resolve; gate green. Deferred: package.json start script.