Base-pin drift: manifest upstream_base_sha stale vs absorbed overlay

[jeonghun-jj-lee]

Base-pin drift: manifest upstream_base_sha is stale vs the absorbed overlay

Problem

The overlay engine was authored against a newer anomalyco/opencode base
than the one the app-bundle manifest pins. packages/app-bundle/manifest.json
records upstream_base_sha = 7fe993879f98aa17cecc70f70d3f40d6f0f11689, but the
overlay's own files expect APIs absent from that base:

• overlaid src/mcp/index.ts declares readonly remove on MCP.Interface
  (and a corresponding server remove endpoint), but base 7fe9938's MCP
  Interface has no remove — so the base-provided test mocks/handlers
  (test/session/snapshot-tool-race.test.ts, test/server/httpapi-mcp-oauth.test.ts,
  and amicode's test/session/prompt.test.ts mock) don't implement it.
• amicode's test/session/llm-native-recorded.test.ts uses
  HttpRecorderInternal.promptAgnosticMatcher, absent from base 7fe9938's
  http-recorder (which is not overlaid, so it materializes at the stale base).

The result is a newer-overlay-on-older-base materialized tree — a Frankenstein
that compiles the binary (so build-binary stays green) but is type-inconsistent
and potentially behavior-inconsistent in non-overlay files. This class of drift
is invisible today precisely because the engine typecheck/test gate was missing
(#1228).

Evidence

• Fork was green on its own test.yml/typecheck.yml, so in the fork these
  APIs existed → the fork's anomalyco base ≠ 7fe9938.
• fork_tag was v1.18.29-amicode.30-67-g8608dcc1 (fork HEAD 8608dcc1).
• Neither cached base (@7fe9938, @v1.18.29) exposes promptAgnosticMatcher
  / MCP remove — the correct base is neither; it must be recovered from
  fork@8608dcc1 history.

Proposed fix (needs its own verification)

1. Determine the anomalyco commit fork@8608dcc1 actually vendored.
2. Bump manifest.json:upstream_base_sha to it; re-run refresh_manifest /
   materialize; confirm drift_gate PASS and the overlay applies cleanly.
3. Revert the symptom-patches added in Restore engine test/typecheck CI coverage (regression gate) #1228 for the now-consistent base
   (the mock remove additions, if the correct base already carries them).
4. Verify the binary still builds and the new engine-tests lane (Restore engine test/typecheck CI coverage (regression gate) #1228) is green.

Acceptance criteria

• upstream_base_sha matches the base the overlay was authored against.
• drift_gate PASS; materialize verifies overlay files at exact hashes.
• Engine bun turbo typecheck green without the Restore engine test/typecheck CI coverage (regression gate) #1228 symptom-patches
  (or with them reduced to genuinely-amicode-owned deltas).
• build-binary still green.

Priority

Not blocking the gate (#1228 patches the symptom to land green), but this is
the correct fix and should follow promptly — a stale base risks other silent
inconsistencies beyond the 4 caught here.

Campaign ledger: sessions/session-20260916-engine-test-ci.md.