feat: make init.jsonc canonical and nudge config drift

[huangzesen]

Summary

• make kernel-owned src/lingtai/init.jsonc the single canonical config-shape source, with explicit canonical/current shapes plus read-only compatibility shapes
• route boot and refresh through one real typed reader with FULLY_EFFECTIVE, READ_OK_WITH_IGNORED_FIELDS, and READ_FAILED outcomes, including safe effective/failure details
• compare local init.json against the canonical/compatibility layers and emit a typed init_config_shape Nudge; never rewrite or migrate the file automatically
• apply the shared global Nudge controls LINGTAI_NUDGE_ENABLED and LINGTAI_NUDGE_REPEAT_INTERVAL to all Nudge kinds
• add the complete environment-variable catalogue and mechanically enforce bidirectional links with every source-derived owning ANATOMY.md
• keep compatibility rationale/retirement conditions in adjacent Contracts and use Git—not a runtime migration registry—as history

Behavior contract

• canonical shape: accepted for current use and new writes
• compatibility-only shape: accepted for reading and reported as a Nudge
• canonical/compatibility conflict: blocked and reported
• unknown/failure: fail closed with repair context and effective fallback when available
• dismissal acknowledges a Nudge; rerunning the same real reader with zero findings resolves it
• no code in this PR mechanically edits init.json

Validation

• fresh exact-head checkout at ffda3739d457df4b5a43c425ac4299364acb4593
• GitHub Native Windows / PowerShell 7: success
• candidate-focused suite: 327 passed; the two remaining failures were classified independently:
  • the vision expectation reproduces unchanged on exact live base a3f172ff571c39792ae219b76611e38feb673de4
  • the preset test passes when the intentionally isolated test HOME is replaced with the normal authenticated HOME
• decisive reader/schema/Nudge/environment-catalogue suite: 125 passed
• combined local integration suite before the final documentation follow-up: 811 passed, 2 known baseline deselections
• changed-module py_compile: PASS
• git diff --check: PASS
• final checkout remained clean
• prior independent Terra review and explicit Claude Opus 4.8 exact-candidate review completed

Scope

This PR owns the kernel reader, canonical shape source, Nudge semantics/policy, prompt/manual guidance, Contracts, Anatomies, and regression gates. The TUI's byte-identical projection and retirement of TUI/Portal runtime migration callers remain in the separate TUI PR.

It does not automatically modify user config, release, deploy, publish, or delete user data.