test: refactor project-management tests to use TestDataFactory and real test DB

- Replace mocked Prisma usage in hierarchy-service.test.ts and prisma-project-service.test.ts with TestDataFactory + getTestDatabase
- Remove vi-based Prisma mocks and mock expectations; import TestDataFactory/PrismaClient and create real test records in beforeEach
- Update tests to assert on created records (ids, fields, event counts) rather than mock call assertions
- Update tools/test-utils TestDataFactory API:
  - change factory methods to accept object params (createWorkspace, createDevlogEntry, createChatSession, createAgentSession)
  - implement createAgentEvent (links agent events to workspace/project)
  - extend createCompleteSetup to accept project/machine/workspace options
- Update IMPLEMENTATION.md to reflect Phase 2 completion and updated test metrics

This shifts these suites from mocked unit tests toward factory-backed integration tests, improving isolation and reliability.

Author: tikazyq