refactor(core): centralize verified run catalog

[ElbertePlinio]

Summary

• add one verified core run catalog for ordered root discovery, duplicate precedence, corrupt-entry handling, and directory/manifest identity binding
• centralize verified root-file reads with symlink, inode, and directory-swap protection
• migrate core listRuns, evidence retention, CLI artifacts, MCP artifact tools, and MCP resources to catalog entries
• keep the current project-local root only; Store run artifacts outside project repositories by default #34 storage modes and migration are intentionally out of scope

Decisions

• manifest runId mismatches fail closed and the entry is omitted
• the first valid duplicate in root-precedence order wins
• equal timestamps use locale-independent run-ID ordering
• genuine missing optional journals remain empty; unsafe or unreadable journals fail closed

Validation

• bun run test packages/core/test/run-catalog.test.ts packages/core/test/run.test.ts packages/core/test/evidence.test.ts (93 passed)
• bun run test packages/mcp-server/test/resources.test.ts packages/mcp-server/test/tools.test.ts (58 passed)
• bun run test packages/cli/test/commands.test.ts (43 passed)
• bun run typecheck
• bun run build
• serious-backend local review plus targeted fix verification: clean

Refs #44 (CAND-3)