The error return (no final_response) was missing history_offset,
falling back to len(history) which has the same session_meta offset
bug fixed in PR #395. Now both return paths include the correct
filtered history length.

…for transcript message extraction

Authored by PercyDikec. Fixes NousResearch#394.

The transcript extraction used len(history) to find new messages, but
history includes session_meta entries stripped before reaching the agent.
This caused 1 message lost per turn from turn 2 onwards. Fix returns
history_offset (filtered length) from _run_agent and uses it for the slice.

The error return (no final_response) was missing history_offset,
falling back to len(history) which has the same session_meta offset
bug fixed in PR NousResearch#395. Now both return paths include the correct
filtered history length.

…for transcript message extraction

Authored by PercyDikec. Fixes NousResearch#394.

The transcript extraction used len(history) to find new messages, but
history includes session_meta entries stripped before reaching the agent.
This caused 1 message lost per turn from turn 2 onwards. Fix returns
history_offset (filtered length) from _run_agent and uses it for the slice.

The error return (no final_response) was missing history_offset,
falling back to len(history) which has the same session_meta offset
bug fixed in PR NousResearch#395. Now both return paths include the correct
filtered history length.

…ll — closes D-kr2-st4 (#14)

emit_kora_event body swap: mcp_client.invoke('kora__append_event', {workspace_id, event_type, payload}) returns substrate event_id. K-9 contract honored. Defensive guards: None mcp_client → ValueError; unexpected response shape → RuntimeError. provider._attempt_chain_event_emit fetches IsoKronMCPClient via KR-7a-wired get_mcp_client(); catches IsoKronMCPInvocationError at lifecycle boundary; ERROR-logs [kora.chain.emit.failed] (operator-visible per PM-lean substrate-side-issue-worth-surfacing). Successful emits INFO-log [kora.chain.emit] with event_id. iso_node_supersede refactored to route kora.node.superseded emit through _attempt_chain_event_emit (unified error handling + cache invalidation surface). Deprecation runway: ChainEventEmitNotAvailableError class kept exported tagged [kora.isokron.deprecated] for one release. Production-test posture: K-9 handler is notImplementedHandler stub on substrate main; dispatch tier (IsoKron task NousResearch#395) un-stubs + bridges Layer-A→Layer-B actor_kind='kora'. KR-7 code shape sound; mock tests pass; production deploys wait. Verify-at-first-live-emit step (actor_id resolution to 0076-seeded canonical Kora actor) documented. ty zero-delta. 351/351 plugins/memory tests pass. Open deferrals 4→3.

…pad MCP call — closes D-kr2-st3

Mechanical follow-on swap unlocked by K-8 (substrate `bd165eb2`) +
KR-7a's MCP client transport. Same pattern as KR-7 chain-emit:
write_scratchpad_entry body replaces `raise
ScratchpadWriteNotAvailableError()` with
`await mcp_client.invoke('kora__write_agent_scratchpad', {...})`,
returning the substrate-assigned scratchpad_entry_id. ~40 LOC across
scratchpad.py + provider.py + tools/iso_node.py + tests + docs.

Production-test posture per IsoKron PM #27:
* K-8's kora__write_agent_scratchpad handler is a
  notImplementedHandler stub on substrate main; dispatch tier (task
  NousResearch#395) un-stubs + bridges Layer-A wsk_* auth → Layer-B actor_kind.
* KR-8 code shape is sound; mock tests verify correctness.
* Production deploys wait on dispatch tier landing — identical
  posture to KR-7 / KR-7b / KR-7a.

K-DG note: K-8's internal flow emits the substrate-canonical chain
literal `kronicle.agent_scratchpad.created` (NOT
`kora.scratchpad.entry.created` as some prior specs may suggest).
The runtime doesn't pass an event_type — the substrate emits
internally as part of the SECDEF flow. Verify-at-first-live-emit:
confirm event_log.actor_id resolves to the 0076-seeded canonical
Kora actor.

scratchpad.py:
* write_scratchpad_entry body: live call to mcp_client.invoke. K-8
  contract output: {'scratchpad_entry_id': '<uuid>',
  'approved_event_id': '<uuid>'} — projected to a plain str
  scratchpad_entry_id return.
* BLAKE3 content_hash computed via existing
  compute_scratchpad_content_hash() helper; passed to MCP tool.
* Defensive: None mcp_client raises ValueError; unexpected response
  shape raises RuntimeError (same pattern as KR-7's emit_kora_event).
* mcp_client param now required (was Optional with deferred-error
  default). Forward signature stays caller-stable from KR-2 ST3.
* ScratchpadWriteNotAvailableError class kept exported tagged
  [kora.isokron.deprecated] for one release. Original deferred-tag
  preserved inside the message for grep stability.

provider.py:_attempt_scratchpad_write:
* Stop catching ScratchpadWriteNotAvailableError (no longer raised).
* Fetch IsoKronMCPClient via self._connection.get_mcp_client();
  failure logs ERROR [kora.scratchpad.write.failed] + returns.
* Catch IsoKronMCPInvocationError + defensive Exception at the
  lifecycle boundary — log at ERROR so failures are operator-visible
  (same posture as KR-7's chain emit). Sessions don't crash; writes
  drop with a loud log line.
* Successful writes log INFO [kora.scratchpad.write] with the
  substrate-assigned entry_id and invalidate the per-workspace
  own-scratchpad cache so the next read re-fetches.

tools/iso_node.py:
* _handle_iso_node_create + _handle_iso_node_supersede: dropped
  the deferred-envelope return path. On success return
  {"ok": True, "entry_id": <substrate-uuid>}. On
  IsoKronMCPInvocationError return
  {"ok": False, "substrate_error": True, "tool_name": ...,
   "message": ...} — structured signal for the model that maps to
  substrate-level failures distinct from validation errors.
* iso_node_supersede also passes the new entry_id into the
  kora.node.superseded chain event payload so audit consumers can
  trace the supersession chain.
* Removed unused ScratchpadWriteNotAvailableError import.

Tests (5 new + 9 updated):
* test_scratchpad.py:
  - Replaced test_write_scratchpad_entry_raises_deferred_write_error
    with 4 MCP-call-path tests (happy/error/None-client/bad-shape)
    + 1 deprecation-runway test.
  - _FakeProviderConnection now exposes get_mcp_client() returning a
    _FakeMcpClient; sync_turn/on_memory_write tests flipped from
    deferred-WARNING assertions to success-INFO + entry_id checks.
  - New test_sync_turn_substrate_error_logs_at_error_session_continues
    verifies the IsoKronMCPInvocationError → ERROR-log path.

* test_iso_node_tools.py:
  - _FakeProviderConnection gains get_mcp_client(); new _FakeMcpClient
    routes by tool_name (kora__write_agent_scratchpad → spe-mock-N;
    kora__append_event → evt-mock-N; kora__read_kora_capability_row
    → minimal matrix).
  - test_iso_node_create_returns_deferred_payload →
    test_iso_node_create_returns_ok_envelope_with_substrate_entry_id;
    new test_iso_node_create_substrate_error_surfaces_structured_envelope.
  - test_iso_node_supersede_inherits_node_kind_from_original flipped
    to assert success + verify the inherited node_kind in the new
    content_inline header + verify the kora.node.superseded emit
    payload carries the new entry_id.

* test_tool_finalize.py: round-trip tests flipped from deferred to
  success-envelope assertions. _FakeProviderConnection gains
  get_mcp_client().

* test_provider_end_to_end.py: _FakeMcpClient extended to handle
  kora__write_agent_scratchpad (returns spe-mock-N). E2E assertions
  flipped from 3 deferred-WARNINGs to 3 [kora.scratchpad.write] INFO
  logs + 3 scratchpad_write_calls on the fake + 2 append_event_calls.
  Assertion narrowed to NOT count the cap-matrix fetch (KR-7b adds
  that; this PR stays narrow per parallel-mergeability).

BUILD_DEVIATIONS:
* D-kr2-st3-no-scratchpad-write-mcp-tool moved Open → Closed with
  Rule-5 spec-quote, KR-8's call-site refactor inventory, production-
  test posture, deprecation-runway note, verify-at-first-live-emit
  step.
* 1 deferral remains open (D-kr3-st2 — KR-9 dispatchable).

README "Operator pitfalls":
* Deferred-surface table trimmed 2 → 1 row (D-kr3-st2 only).
* D-kr2-st3 moves to Recently-closed list.
* Individual "Scratchpad writes are currently deferred" pitfall
  rewritten as "Scratchpad writes route via kora__write_agent_
  scratchpad (KR-8)" with success/failure log paths + operator
  grep pointer.

Local gates:
* ty check — 7,337 diagnostics, zero-delta vs KR-7 baseline.
* pytest tests/plugins/memory/ — 357/357 passing.
* Full suite via xdist (-n auto): 24,654 / 168 failed / 129 skipped.
  Δ vs KR-7b (24,652/175/129): +2 passed, -7 failed. Same
  tests/tools/* + tests/tui_gateway/* xdist isolation noise; none
  touch isokron.

1 deferral still open pending CC#1 substrate:
* D-kr3-st2-no-relationlink-write-mcp-tool ← KR-9 (K-10 merged; PM dispatched)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…pad MCP call — closes D-kr2-st3 (#16)

Mechanical follow-on swap unlocked by K-8 (substrate bd165eb2) + KR-7a's MCP client transport. Same pattern as KR-7 chain-emit: write_scratchpad_entry body replaces raise ScratchpadWriteNotAvailableError with await mcp_client.invoke('kora__write_agent_scratchpad', {...}), returning the substrate-assigned scratchpad_entry_id. Production-test posture per IsoKron PM #27: K-8 handler is notImplementedHandler stub on substrate main; dispatch tier (task NousResearch#395) un-stubs + bridges Layer-A→Layer-B; KR-8 code-shape sound; mock tests verify correctness; production deploys wait on dispatch tier. K-DG note: substrate-canonical chain literal kronicle.agent_scratchpad.created (NOT kora.scratchpad.entry.created). ScratchpadWriteNotAvailableError class kept exported tagged [kora.isokron.deprecated] for one release. Defensive guards: None mcp_client → ValueError; unexpected response shape → RuntimeError. tools/iso_node.py iso_node_create + iso_node_supersede dropped deferred-envelope return path; on success returns {ok:true, entry_id}; on IsoKronMCPInvocationError returns {ok:false, substrate_error:true, tool_name, message}. 5 new + 9 updated tests; ty zero-delta; 357/357 plugins/memory tests pass. Cherry-pick rebased onto post-KR-7 + KR-7b main.

…ink MCP call — closes D-kr3-st2

Fourth + final mechanical follow-on swap unlocked by K-10 + 0083
(IsoKron PM #32). Same pattern as KR-7 (chain-emit) and KR-8
(scratchpad-write): create_relationlink body replaces `raise
RelationLinkWriteNotAvailableError()` with
`await mcp_client.invoke('kora__create_relationlink', {...})`,
returning the substrate-assigned link_id. ~30 LOC across
relationlink.py + tools/iso_link.py + tests + docs.

All three KR-3 ST2 substrate blockers are now resolved substrate-side:
* actor_kind CHECK extended to include 'kora' via 0083 (prod-applied)
* public.kora_create_relationlink SECDEF function exists
* kora.relationlink.created event literal in event_log_event_type_check
  (300th literal in the set post-0083)
* kora__create_relationlink Sea MCP tool registered

Production-test posture per IsoKron PM #27:
* K-10's kora__create_relationlink handler is a notImplementedHandler
  stub on substrate main; substrate-team's dispatch tier (task NousResearch#395)
  un-stubs + bridges Layer-A wsk_* auth → Layer-B actor_kind='kora'.
* KR-9 code shape is sound; mock tests verify correctness.
* Production deploys wait on dispatch tier landing — identical
  posture to KR-7 / KR-7b / KR-8.

Verify-at-first-live-emit per spec § 3:
* event_log row with event_type = 'kora.relationlink.created'
* event_log.actor_id = 0076-seeded canonical Kora actor (NOT
  token-UUIDv5)
* relationlink row with chain_event_id matching the emitted event +
  created_by_actor_kind = 'kora'

relationlink.py:
* create_relationlink body: live call to mcp_client.invoke. K-10
  contract output: {'link_id': '<uuid>', 'chain_event_id': '<uuid>'}
  — projected to a plain str link_id return.
* mcp_client param now required (was Optional with deferred-error
  default).
* New rationale_block_id + evidence_block_ids params match K-10's
  input schema. Legacy `rationale` parameter preserved for one-
  release back-compat (silently dropped — superseded by
  rationale_block_id).
* Defensive: None mcp_client → ValueError; unexpected response shape
  → RuntimeError (mirrors KR-7/KR-8 pattern).
* RelationLinkWriteNotAvailableError class kept exported tagged
  [kora.isokron.deprecated] for one release. Original three-blocker
  message preserved inside the message body for grep stability.

tools/iso_link.py:_handle_iso_link_create:
* Dropped the deferred-envelope path. Success →
  {"ok": True, "link_id": <substrate-uuid>}. Substrate failure →
  {"ok": False, "substrate_error": True, "tool_name", "message"} —
  same structured signal shape as KR-8's iso_node_create.
* Fetches IsoKronMCPClient via get_mcp_client(); MCP-client-
  unavailable returns {"ok": False, "error": ...} envelope.
* Removed unused RelationLinkWriteNotAvailableError import.

Tests (7 new + 2 updated):
* test_iso_link_tools.py:
  - test_create_relationlink_raises_deferred_write_error →
    test_create_relationlink_invokes_kora__create_relationlink:
    happy path asserts spec-pinned arg shape (workspace_id,
    from/to entity_id + kind, link_type, evidence_block_ids=[]).
  - New test_create_relationlink_propagates_mcp_invocation_error
    (substrate active-edge uniqueness violation surfaces).
  - New test_create_relationlink_rejects_none_mcp_client.
  - New test_create_relationlink_rejects_unexpected_response_shape.
  - New test_create_relationlink_passes_rationale_block_id_when_present
    (optional args pass-through).
  - New test_relationlink_write_not_available_error_still_importable_post_kr9
    (deprecation runway).
  - test_iso_link_create_handler_returns_deferred_envelope →
    _returns_ok_envelope_with_substrate_link_id: success-envelope
    + verifies spec-pinned tool name in invoke recording.
  - New test_iso_link_create_handler_surfaces_substrate_error_envelope:
    IsoKronMCPInvocationError flips to structured envelope.
  - _FakeMcpClient routes by tool_name (returns link-N for
    kora__create_relationlink). _FakeProviderConnection gains
    get_mcp_client().

BUILD_DEVIATIONS:
* D-kr3-st2-no-relationlink-write-mcp-tool moved Open → Closed with
  Rule-5 spec-quote, call-site refactor inventory, production-test
  posture, all-three-blockers-resolved-substrate-side note,
  deprecation-runway note, verify-at-first-live-emit step.

README "Operator pitfalls":
* "Deferred-surface summary" table replaced with
  "All BUILD_DEVIATIONS closed code-side as of KR-9 (parallel-merged
  with KR-7b + KR-8)" note. All 5 deferral closures listed under
  Recently closed.
* Individual "iso_link_create writes are blocked" pitfall rewritten
  as "RelationLink writes route via kora__create_relationlink (KR-9)"
  with success/failure envelope shapes + operator grep pointer.

Parallel-mergeability note: KR-7b + KR-8 + KR-9 modify disjoint files
(KR-7b: capability_matrix_mirror.py + provider.initialize; KR-8:
scratchpad.py + provider sync_turn/on_memory_write; KR-9:
relationlink.py + tools/iso_link.py). Merge interleaves; each PR
narrows its E2E assertions to its own surface so test fixture
counts don't fight. PM handles README + BUILD_DEVIATIONS final
reconciliation on merge order.

Local gates:
* ty check — 7,337 diagnostics, zero-delta vs KR-7 baseline.
* pytest tests/plugins/memory/ — 357/357 passing.
* Full suite via xdist (-n auto): 24,629 / 181 failed / 12 errors /
  129 skipped. Same tests/tools/* xdist isolation noise as documented
  across prior PRs; none touch isokron.

After KR-9 + KR-7b + KR-8 merge, all four BUILD_DEVIATIONS are
closed code-side. Standing-by state becomes dispatch-tier-gated
(waiting on substrate-team task NousResearch#395 + service-token mint for
production deploys).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…ink MCP call — closes D-kr3-st2 (#17)

4th and FINAL mechanical closure swap. Mechanical follow-on swap unlocked by K-10 (substrate 35e67f18 + 0083 applied to prod) + KR-7a's MCP client transport. create_relationlink body replaces raise NotAvailableError with await mcp_client.invoke('kora__create_relationlink', {...}). Production-test posture: K-10's kora__create_relationlink handler is notImplementedHandler stub on substrate main; dispatch tier (task NousResearch#395) un-stubs. Forward-stability touch: added rationale_block_id + evidence_block_ids params matching K-10 input schema; legacy rationale param preserved for one-release back-compat (silently dropped — superseded by rationale_block_id). Original exception class kept exported tagged [kora.isokron.deprecated]. Verify-at-first-live-emit: event_log.actor_id resolves to 0076-seeded canonical Kora actor; public.relationlink row chain_event_id matches; created_by_actor_kind='kora'. ty zero-delta; 357/357 plugins/memory tests pass. Cherry-pick rebased onto post-KR-8 main. ALL 4 Kora-runtime BUILD_DEVIATIONS now closed code-side.

…for transcript message extraction

Authored by PercyDikec. Fixes NousResearch#394.

The transcript extraction used len(history) to find new messages, but
history includes session_meta entries stripped before reaching the agent.
This caused 1 message lost per turn from turn 2 onwards. Fix returns
history_offset (filtered length) from _run_agent and uses it for the slice.

The error return (no final_response) was missing history_offset,
falling back to len(history) which has the same session_meta offset
bug fixed in PR NousResearch#395. Now both return paths include the correct
filtered history length.