Sync phase 1: upstream v0.9.29 bugfixes onto chronode main - #5

…itg00#1132)

* fix(memory): guard mem::forget delete/count on record existence

Calling mem::forget with a lesson id (lsn_*) deleted a nonexistent key
from the memories keyspace, counted it, and reported success. Guard the
delete, index cleanup, and counter on the kv.get result, matching the
mem::governance-delete pattern, so nonexistent ids return
{ success: true, deleted: 0 } with no audit row. Closes rohitg00#1120.

* feat(lessons): add mem::lesson-delete soft-delete function

Register mem::lesson-delete to set deleted: true on a lesson, mirroring
the lesson-strengthen existence guard and audit pattern. Read paths
already filter !l.deleted, and re-saving deleted content creates a fresh
lesson. Adds lesson_delete to the audit operation union.

* feat(mcp): expose memory_lesson_delete tool and REST endpoint

Wire mem::lesson-delete through the MCP tool registry and dispatch
case (memory_lesson_delete) and a POST /agentmemory/lessons/delete REST
route with 400 for a missing lessonId and 404 for a nonexistent lesson.

* chore(consistency): bump tool/endpoint counts to 54/129

Adds memory_lesson_delete to the registry, so update every count surface:
tool-count test, README badge and prose, AGENTS.md stats,
INSTALL_FOR_AGENTS.md, plugin manifests and docs, and the two code
comments this change makes stale. REST endpoint count goes 128 to 129
for the new /agentmemory/lessons/delete route.

* refactor(lessons): simplify 404 mapping and restore decay-delta test

Cast the lesson-delete trigger result once instead of twice inline, and
restore the lastDecayedAt incremental-delta decay test that was dropped
when the lesson-delete describe block was added.

* fix(review): align 404 error shape and regenerate skill references

Review fixes: the lesson-delete REST route now returns the repo-standard
{ error: 'lesson not found' } body on 404 instead of the function-shaped
{ success: false } payload, matching api::memory-by-id. Regenerated the
autogen MCP and REST skill references so memory_lesson_delete and the
lessons/delete route appear in the tables with accurate counts.

* fix(lessons): normalize lessonId at entry points and harden no-op test

Address CodeRabbit review: trim lessonId once at both the MCP dispatch
and REST route before triggering mem::lesson-delete (whitespace-padded
ids previously 404'd or looked up raw), and extend the nonexistent-
memoryId regression test to assert the no-op path performs no kv.delete
and no search-index cleanup.

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Co-authored-by: Rohit Ghumare <48523873+rohitg00@users.noreply.github.com>

Restore the memory_lesson_delete registry definition lost in conflict
resolution, bump every count surface (test constant, README badge and
prose, plugin manifests, AGENTS.md, autogen skill references, code
comments) from the drifted 58/59 to the measured 60, and regenerate
skill references so the generator output matches hand-resolved content.

Port of upstream rohitg00#908 fix (a2a2af9, subset): initialize echoes the
client's requested revision when it is one we support and answers with
the newest supported revision otherwise, so hosts requiring a newer MCP
revision stop disconnecting with -32000. Strict tool discovery and the
local fallback policy are unchanged; four handshake tests pin the wire
behavior.

The cherry-picked REST registration bypassed registerApiTrigger, so the
route shipped without middleware::api-auth and failed the
every-route-protected invariant. Also refresh the generated interface
inventory for the new route.

mcp-standalone.test.ts gained the initialize negotiation block; the
tracked-tests list is unchanged, so only content_sha256 moves.

README prose, the banner-adjacent toolkit line, AGENTS.md stats, the
boot banner in src/index.ts, and the generated interface inventory now
agree with the registered route table.

The interface-inventory gate hardcoded pre-sync counts; align it with
the regenerated inventory so CI matches the reconciled surfaces.

The committed hook bundles are build outputs; CI rebuilds them and the
stale shim made the R13 runner see a dirty worktree. Rebuilt via
npm run build after the protocolVersion change.