Authorship grounding: fix issue #29 across emit, memory, tools, and prompts - #32

Merged

ahueb merged 203 commits into

issue-29-authorship-grounding

Aug 14, 2026

Commits on Jul 15, 2026

Add cohort agent isolation + reactive-priority scheduler

malanjary-tsri
and
claude
committed
b00b0e6

Commits on Jul 20, 2026

Stage 1+2: make DB the primary conversation store (Slack-off content + rebuild)

malanjary-tsri
and
claude
committed
a7659b4
Stage 3: transport abstraction + slack_enabled flag + DB inbox poller

malanjary-tsri
and
claude
committed
131104f
Stage 4: Slack-less private-channel migration + generalize DB inbound poller

malanjary-tsri
and
claude
committed
5b0c953
Stage 5: PI web interface for messaging agents without Slack

malanjary-tsri
and
claude
committed
cd072b9
Stage 6: guard secondary Slack posters + record Slack-mirror mapping

malanjary-tsri
and
claude
committed
c8500cd
Stage 7: DM persistence (migration 0020) + web DMs + one-time Slack backfill

malanjary-tsri
and
claude
committed
33d31cb

Commits on Jul 21, 2026

Fix: import AgentChannel in simulation (Stage 2 _persist_seeded_channels)

malanjary-tsri
and
claude
committed
771b655
Populate slack_ts on inbound-polled human messages

malanjary-tsri
and
claude
committed
09041a1
Merge remote-tracking branch 'origin/main' into db-primary-conversations
malanjary-tsri
committed
c840642
Align db-primary branch to the new test-suite layout

malanjary-tsri
and
claude
committed
311deba
test: integration coverage for the DB-native PI inbox

malanjary-tsri
and
claude
committed
1bfb170

Commits on Jul 24, 2026

H1: re-queue failed message-log flush instead of dropping it

andrewsu
and
claude
committed
79390d0
mint precision + M1: unique ts-shaped ids and human-row-safe upsert

andrewsu
and
claude
committed
b4a0e14
H2: stop the inbox cursor from permanently skipping a PI message

andrewsu
and
claude
committed
0728ce7
B1/B2: bound the per-tick COUNT and the startup state rebuild

andrewsu
and
claude
committed
3053fba
M2: make the channel-cache a Transport contract; drop dead code

andrewsu
and
claude
committed
9548c08

Commits on Jul 25, 2026

R1/R2/R3: close the durability + cross-process gaps Slack used to cover

malanjary-tsri
and
claude
committed
33659a8
Order thread history by posted_at; never hand a canonical id to Slack

malanjary-tsri
and
claude
committed
a93d136

Commits on Jul 26, 2026

R4/R5: persist the private-channel handover in both migration paths

malanjary-tsri
and
claude
committed
2a2e98c
Order every "most recent" MessageLog read by posted_at, not by insertion

malanjary-tsri
and
claude
committed
baa5583
Record the Slack mirror mapping on polled bot messages

malanjary-tsri
and
claude
committed
7d8b177
Stop inferring slack_ts from the channel id; repair legacy rows instead

malanjary-tsri
and
claude
committed
10c240c

Commits on Jul 27, 2026

Merge pull request #19 from SuLab/db-primary-conversations
malanjary-tsri
authored
b7edcbc

Commits on Jul 30, 2026

Merge cohort-agent-isolation into the DB-primary conversation store
ahueb
committed
8e7536e
Implement cohort system v2 on the DB-primary conversation store

ahueb
and
claude
committed
8489a31
Add live end-to-end cohort tests; verify the suite by mutation

ahueb
and
claude
committed
a5fffb4
Browser, concurrency, 20-agent and real-API testing; long-run plan

ahueb
and
claude
committed
ac6dfd2
Real-API cohort tests: fix two vacuous designs the API exposed

ahueb
and
claude
committed
d679ae6
Fix two gate defects a real multi-turn run surfaced

ahueb
and
claude
committed
ad9edbb
Ignore .playwright-mcp/ browser artifacts

ahueb
and
claude
committed
f0fb218
Tasks 1-2: exhaustive §5.1 and §5.3 tables, each with a polarity control

ahueb
and
claude
committed
6a00188
Task 3: pilot-scale gate recompute and mid-run roster churn

ahueb
and
claude
committed
103a030
Task 4: pin forward-only cursor semantics (§6.3)

ahueb
and
claude
committed
2d4ea8f
Task 5: §7 exemption through all three write paths

ahueb
and
claude
committed
439f9b3
Task 6: §8 both halves in one test; §13.1 snapshot through start()

ahueb
and
claude
committed
6dbef70
Task 7: parametrised strip table with survival controls; valve at 20 agents

ahueb
and
claude
committed
fc3c7ac
Task 8: §11 settings-cached vs membership-live, and matrix save safety

ahueb
and
claude
committed
7280194
Task 9: pin the alembic CI gate; add an opt-in migration round trip

ahueb
and
claude
committed
71d4111
Task 10: real-API open-policy and non-transitivity, each controlled

ahueb
and
claude
committed
c9db0f6
Tasks 11-12: real multi-turn scenario harness and five scenarios

ahueb
and
claude
committed
3fccf35
Task 13: mutation check for the cohort gate — 9/9 killed

ahueb
and
claude
committed
3ecb934

Commits on Jul 31, 2026

Slack T1: token validity, source precedence, slack_enabled tri-state

ahueb
and
claude
committed
033ddf3
Slack T2: client wire contract + provisioning; two production bugs fixed

ahueb
and
claude
committed
9dbc9e0
Slack T0/T3/T4: live tier wired up; 20 tests against the real workspace

ahueb
and
claude
committed
cad3683
Slack T5: the DB<->Slack mirror, live — all four recent fixes confirmed

ahueb
and
claude
committed
147e458
Slack T9: the cohort gate x the Slack mirror, live

ahueb
and
claude
committed
e97f989
Slack T6/T10/T11: restart, off<->on transitions, failure modes

ahueb
and
claude
committed
e5979cf
Slack T7: PI interaction over real Slack with the real classifier

ahueb
and
claude
committed
abb1f89
Slack T8: private-channel migration against the real workspace

ahueb
and
claude
committed
56507cb
Slack T12: teardown, mirror mutation check, and flake fixes

ahueb
and
claude
committed
b17a8cc
Remove a real-token prefix from a test fixture

ahueb
and
claude
committed
b4a450b
Full-system T0/T1: live_api tier and ORCID, with fixture-drift detection

ahueb
and
claude
committed
acadc96
Full-system T2/T3: PubMed and grants.gov live; real drift found

ahueb
and
claude
committed
58f181f
Full-system T6: the CLI, 7 commands, 15 passed / 2 xfailed

ahueb
and
claude
committed
5285b81
Full-system T11: the proposal review loop, 17 passed

ahueb
and
claude
committed
ed85a21
Full-system T9: public routes — no private leak, window edges pinned

ahueb
and
claude
committed
895709f
Full-system T5: the worker, 15 passed — and a silent job-loss path

ahueb
and
claude
committed
d732804
Full-system T8: agent page, 84 passed / 3 xfailed — a privacy hole

ahueb
and
claude
committed
c6e39dd
Full-system T7: onboarding/profile/settings, 73 passed — no auth holes

ahueb
and
claude
committed
cf16665
Full-system T4: profile pipeline live — grounding proved empirically

ahueb
and
claude
committed
f6842cd
Full-system T10: GrantBot live — every funding post is a title inference

ahueb
and
claude
committed
c3b01cc
T14: independent mutation check — 11/13 killed, two real survivors

ahueb
and
claude
committed
6cecb65
Live Slack tier: deterministic — the flakiness was a production bug

ahueb
and
claude
committed
d0f4ed4
T12: browser flows driven; provisioning verified end to end from Slack

ahueb
and
claude
committed
c652fcc
T13: the whole system running — Slack silently splits >4000-char messages

ahueb
and
claude
committed
351676a
WIP: four fixes implemented offline-green; live Slack tier UNVERIFIED

ahueb
and
claude
committed
d311170
Fix a missing `import re` the pre-push gate caught

ahueb
and
claude
committed
ac5b354
Verify fixes 1-3: all three have teeth; my baseline figure was wrong

ahueb
and
claude
committed
35ff4bf
Drop an unused `json` import Fix 2 added

ahueb
and
claude
committed
5d8571a
Fix 4 verified: chokepoint closes all four defects; it also had three of its own

ahueb
and
claude
committed
8515f65

Commits on Aug 4, 2026

docs: ship the cohort spec the code actually cites

ahueb
and
claude
committed
16136a1
feat: add slack_web, the Slack boundary for the web layer

ahueb
and
claude
committed
22d2606
test: pin the _MAX_POST_CHARS invariant that holds defect 2 closed

ahueb
and
claude
committed
d5f8574
fix: make _rebuild_agent_state idempotent, and characterise the live failure

ahueb
and
claude
committed
02f5749
fix: CLI exits nonzero on unknown ORCID, and the backfill is idempotent

ahueb
and
claude
committed
da405cb
test: cover the cohort admin routes' remaining branches

ahueb
and
claude
committed
c3a0e1a
fix: split GrantBot's posts, and route it through the Slack boundary

ahueb
and
claude
committed
ae12344
feat: post_message takes thread_ts, so threaded callers can use the boundary

ahueb
and
claude
committed
5ec66d2
fix: close the Slack boundary, the privacy hole, and two identity defects

ahueb
and
claude
committed
02143de
fix: delete the dead onboarding path and the broken profile link

ahueb
and
claude
committed
d1005b1
chore: clear the lint debt this branch added, and fix the coverage tracer

ahueb
and
claude
committed
bd68fae
chore: widen the local gate to src lint and the alembic round trip

ahueb
and
claude
committed
cc8490f
chore: one mutation isolation strategy, and headers that match measurement

ahueb
and
claude
committed
5aeb558
chore: ignore docs/superpowers/, the plan/scratch working directory

ahueb
and
claude
committed
85a7fea
fix: keep the Slack boundary off the event loop

ahueb
and
claude
committed
fa143a6
fix: make the grants.gov contract match what grants.gov actually sends

ahueb
and
claude
committed
afe7733
test: a partial probe-bot set skips the live Slack tier, it does not fail it

ahueb
and
claude
committed
46e66fe
fix: unblock probe-bot provisioning — omittable scopes, and correct container names

ahueb
and
claude
committed
7ac0224
fix: a refresh token alone is enough to provision, and say so when it is dead

ahueb
and
claude
committed
ae18cdb
fix: the live Slack tier is green — Slack escapes <, >, & and the mirror does not

ahueb
and
claude
committed
f017572
test: make the no-token assertions hermetic against a provisioned .env

ahueb
and
claude
committed
56c7d48

Commits on Aug 5, 2026

fix: answer a missing cohort the same way everywhere, and drop a dead context key

ahueb
and
claude
committed
356454f
test: run the e2e tier for the first time, and give the mirror harness teeth

ahueb
and
claude
committed
cd2bd66
fix: the slack_ts backfill mis-verified every thread reply

ahueb
and
claude
committed
cb4378b
chore: widen the migration round trip to 0018, where the downgrades have teeth

ahueb
and
claude
committed
52de34a
fix(db): bound the migration's lock wait instead of letting it stall forever

ahueb
and
claude
committed
fa2c442
fix(web): give the message and DM listings a total ordering

ahueb
and
claude
committed
69fc607
feat(migrate): guided, verified migration path to 0023 from 0018 or 0019

ahueb
and
claude
committed
28d53b7
fix(migrate): accept 0020 and 0021, which is where a deployment tracking main is

ahueb
and
claude
committed
5fa6219

Commits on Aug 10, 2026

docs(spec): org1 parity — the generic blackbird work, minus the product

ahueb
and
claude
committed
3411664
docs(spec): correct the test_roles.py mechanism — nothing is trimmed

ahueb
and
claude
committed
9d11ec0
docs(spec): the Scripps guard needs no edit — 0e1ac52 is what breaks it

ahueb
and
claude
committed
17085f5
docs(plan): implementation plan for the org1 parity port

ahueb
and
claude
committed
d57b70a
docs(plan,spec): fold in the adversarial-audit amendments

ahueb
and
claude
committed
5f720aa
Merge remote-tracking branch 'origin/copi-prod' into org1-parity

ahueb
and
claude
committed
74abdc3
chore: clear unused imports and pin three settings-dependent tests

ahueb
and
claude
committed
d2abb1a
feat(roles): prompt-path resolution with per-role fallback

Ubuntu
authored and
ahueb
committed
1d55515
feat(roles): role.toml manifest with tool allow-list and safe fallbacks

Ubuntu
authored and
ahueb
committed
c56113e
refactor(agent): role-aware prompt loading; collapse 3 builders into 1; extract identity to file

Ubuntu
authored and
ahueb
committed
255d429
feat(db): add agents.role column (migration 0024)

Ubuntu
authored and
ahueb
committed
599d71a
fix(migrate): advance migration tooling's target from 0023 to 0024

Ubuntu
authored and
ahueb
committed
c70b48b
feat(roster): thread role through roster reads; pick up role changes live

Ubuntu
authored and
ahueb
committed
3250aa6
feat(tools): per-role tool allow-list, enforced in Phase 4 and the executor

Ubuntu
authored and
ahueb
committed
74ecbd2
fix(cohort): scope lab directory to the cohort gate (runbook A3)

Ubuntu
authored and
ahueb
committed
a02a781
feat(admin): view and set agent role; show role on topology page

authored and
ahueb
committed
d8341c4
test(admin): give the role-set test a tmp roles dir — org1 ships no prompts/roles

ahueb
and
claude
committed
24823c8
fix(agent): phase 5 must honour role prompt overrides like every other phase

ahueb
and
claude
committed
7ed24bc
fix(migrate): plan and verify 0024's column, and pin the head to it

ahueb
and
claude
committed
2db3dbb
chore: drop three unused imports the role refactor left behind

ahueb
and
claude
committed
5f7ec0e
fix(ci): drop test_roles.py's unused pathlib import — it fails the tests/ gate

ahueb
and
claude
committed
f9d9685
docs(plan): the Path-import fix must precede CHECKPOINT 1, not ride Task 9

ahueb
and
claude
committed
11eeadf
docs: design for cohort-scoped conversations feed, threads, topology payload

authored and
ahueb
committed
e6aa237
docs: implementation plan for cohort-scoped feed, threads, topology payload

authored and
ahueb
committed
91469fe
fix(admin): topology matrix payload 3,360 fields -> 116

Ubuntu
authored and
ahueb
committed
743374b
fix(admin): bound the topology cross product by table size, not payload size

Ubuntu
authored and
ahueb
committed
cb1cd0e
feat(feed): gate_clause — the cohort gate as a SQL predicate

Ubuntu
authored and
ahueb
committed
02443ca
feat(feed): resolve_agent_gate via the engine's compute_gates

Ubuntu
authored and
ahueb
committed
39ccbe3
docs(feed): clarify resolve_agent_gate docstrings post-review

Ubuntu
authored and
ahueb
committed
2403b1a
fix(feed): cohort-scope the conversations page and select thread roots

Ubuntu
authored and
ahueb
committed
0c2e792
fix(feed): own-post carve-out, gate the reply count, and pin the regressions

Ubuntu
authored and
ahueb
committed
7637651
feat(feed): thread expand endpoint returning a gated replies partial

authored and
ahueb
committed
c22f3f1
fix(feed): prove replies are actually gated; dedupe channel-set computation

authored and
ahueb
committed
87c3f64
feat(feed): render roots with a reply badge and expand-on-click

authored and
ahueb
committed
ddd9a40
fix(feed): guard the thread-expand link against a double-click mid-fetch

authored and
ahueb
committed
edb5a7a
fix(feed): cover the plural badge and href correctness gaps from review

authored and
ahueb
committed
1e43699
docs(cohort): correct spec/docstrings now that the PI feed is gated (F1, F6, F7)

authored and
ahueb
committed
354b937
fix(feed): scope reply queries to the root's channel; log preflight fail-open (F2-F4)

authored and
ahueb
committed
16b0113
test(admin): pin the topology marker/cell cross-product invariant (F5)

authored and
ahueb
committed
f842aa7
docs(cohort): fix the amendment pointer to specs/, not .notes/

authored and
ahueb
committed
d31e754
docs(spec): load-proportional budget and scheduling for star topologies

authored and
ahueb
committed
6d8731a
docs(plan): implementation plan for load-proportional budget/scheduling

authored and
ahueb
committed
c4f4753
docs(plan): adversarial audit against HEAD 7f6b304 — fix 4 defects

authored and
ahueb
committed
4315607
feat(sched): _agent_load — the shared load signal

Ubuntu
authored and
ahueb
committed
2646248
feat(config): rate-limiter settings + optional per-role allowance

Ubuntu
authored and
ahueb
committed
e64095c
feat(sched): call ledger — record_api_call maintains both counters

Ubuntu
authored and
ahueb
committed
f2efbd9
fix(roster): adopt a Slack client when a live agent gains a token

authored and
ahueb
committed
d1c440e
feat(sched): sliding-window rate limiter replaces the cumulative cap

Ubuntu
authored and
ahueb
committed
05e867d
feat(sched): rebuild call_times from llm_call_logs within the window

Ubuntu
authored and
ahueb
committed
ec03683
fix(sched): make step 4b idempotent and DB-test the window query

Ubuntu
authored and
ahueb
committed
24b4b02
feat(sched): load-proportional selection weight and reactive tiebreak

Ubuntu
authored and
ahueb
committed
18c6f8c
feat(cli): deprecate --budget, default it off, document the replacement

authored and
ahueb
committed
9ededfe
test(sched): production regression for the run-4f1e8395 hub bench

Ubuntu
authored and
ahueb
committed
1146586
fix(ci): make settings-dependent tests hermetic; clear lint debt

authored and
ahueb
committed
3e7f104
fix(sched): a throttled roster must back off, not end the run (F1-F5, F7)

authored and
ahueb
committed
1754415
fix(agent): phases 2 and 4 must honour role prompt overrides like every other phase

Ubuntu
authored and
ahueb
committed
0e473f5
fix(agent): phase2-prune must also honour role prompt overrides

Ubuntu
authored and
ahueb
committed
38d8952
feat(scout_hub): drive the interview off the screening rubric, not the collaboration script

Ubuntu
authored and
ahueb
committed
10daf36
fix(llm): detect and log a still-truncated retry; let callers count it

authored and
ahueb
committed
f5fad2c
fix(sched): suppress a post that strips to nothing, and tell the caller

ahueb
and
claude
committed
6af8207
fix(admin): a Slack post with no mappable sender must not 500 /admin/discussions

ahueb
and
claude
committed
f2a9e4f
fix(admin,public): close the null-agent_id 500 class, an unauthenticated vote-tamper hole, and a false assessment-persist failure

ahueb
and
claude
committed
c145abe
fix(llm): finish the truncation fix — generate_with_tools had the same defects

ahueb
and
claude
committed
35e9bf9
fix(agent): a suppressed post must not count as a turn

ahueb
and
claude
committed
2d02879
fix(phase5): a response with no `action` is unparseable, not a new post

ahueb
and
claude
committed
4cf7bd5
fix(cohort): build the lab directory after the gate, not before

ahueb
and
claude
committed
16064fe
feat(post_types): the canonical vocabulary and the role+topology filter

ahueb
and
claude
committed
5f12ea7
feat(post_types): add legacy idea->idea_crosslab alias resolution

ahueb
and
claude
committed
824b1fe
feat(roles): parse a post_types allow-list from role.toml

ahueb
and
claude
committed
1d89e2e
feat(agent): substitute {post_type_menu} in the phase-5 prompt

ahueb
and
claude
committed
58b58d2
fix(post_types): dedupe duplicate entries; keep the directory on a gate failure

ahueb
and
claude
committed
8f4f95b
docs(spec): land the post-type gating design, without the draft prompt tree

ahueb
and
claude
committed
036f286
docs(plan): Task 19's measured counts — 76 commits, 11 Ported-from trailers

ahueb
and
claude
committed
e6a5c40
Merge prod's live copi-prod state (3e3c379) — the unpushed logging override

ahueb
and
claude
committed
fa47e30
feat(llm): upgrade the agents to Claude Opus 5

ahueb
and
claude
committed
d4ee439

Commits on Aug 11, 2026

fix(email): harden inbound reply processing against the failures found in the prod investigation

ahueb
and
claude
committed
8f96f86
fix(email): only solicit replies when the inbound pipeline is enabled

ahueb
and
claude
committed
1284042
ops(email): inbound infrastructure check/provision script + runbook

ahueb
and
claude
committed
86568bf
feat(agent): authorship-claim validators grounded in publication records (#29)

ahueb
and
claude
committed
022d696
feat(agent): strip ungrounded authorship lines from memory syntheses (#29)

ahueb
and
claude
committed
3bcd8d9
fix(test): replace tautological or-ed assertion with single exact assertion

ahueb
and
claude
committed
1865644
feat(agent): load publications-table ground truth per agent at roster sync (#29)

ahueb
and
claude
committed
4e4da5e
fix(agent): isolate publication-record load failures from the roster sync (#29)

ahueb
and
claude
committed
6e0c509
feat(agent): authorship emit gate on phase 4/5 and _post_message, fail-closed (#29)

ahueb
and
claude
committed
fabc1e4
feat(tools): retrieve_abstract/full_text return the PubMed author list (#29)

ahueb
and
claude
committed
ed734f3
feat(agent): strip ungrounded authorship claims at memory synthesis (#29)

ahueb
and
claude
committed
b6c2de4
test(tools): pin PubMed author parsing branches and full_text Authors line (#29)

ahueb
and
claude
committed
9dfd004
feat(prompts): close the authorship honesty gap in system/phase-4/phase-5 prompts (#29)

ahueb
and
claude
committed
5a4e6f1
ops(agent): one-time sweep for poisoned authorship memories (#29)

ahueb
and
claude
committed
a83060e
fix(agent): sweep legacy flat memory layout and survive per-file errors (#29)

ahueb
and
claude
committed
80655ec
docs: prod remediation runbook for issue #29

ahueb
and
claude
committed
86ea08f
fix(agent): close the paraphrase fail-open in first-person claim detection (#29 audit C1, M1)

ahueb
and
claude
committed
6244934
fix(agent): joint-authorship synonyms + claim-scoped DOI grounding (#29 audit I2, I3)

ahueb
and
claude
committed
8aad473
fix(agent): gate before tag-strip in phase 5; resolve prose-named co-author labs (#29 audit I1, I4)

ahueb
and
claude
committed
48d0c16
fix(agent): identity-aware memory strip — no laundering through third-person subjects (#29 audit I5)

ahueb
and
claude
committed
12f7b46
fix(sweep): ground the sweep in DB ∪ profile DOIs, like the runtime guard (#29 audit I6)

ahueb
and
claude
committed
bc3464a
fix(agent): exclude Slack's label pipe from DOI extraction (#29 audit M2)

ahueb
and
claude
committed
a90e4a3
feat(tools): surface the paper's DOI in retrieve_abstract/retrieve_full_text (#29 audit O-I3)

ahueb
and
claude
committed
2d804b0
test(agent): pin the phase-4/phase-5 authorship gate call sites and backoff (#29 audit O-I4)

ahueb
and
claude
committed
57cf339
docs(runbook): sweep with agent-run stopped; real verification signals; muted-labs note (#29 audit O-runbook)

ahueb
and
claude
committed
b1d54da

Commits on Aug 12, 2026

fix(llm): keep the high-volume agent paths on the Sonnet tier

ahueb
and
claude
committed
aaba04b
Merge branch 'org1-parity' into email-fix
ahueb
committed
98fbb21
Merge branch 'email-fix' into issue-29-authorship-grounding
ahueb
committed
3324eb2