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feat: SA Multi-Language Comparison node, endpoint, and dashboard action#43

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feat: SA Multi-Language Comparison node, endpoint, and dashboard action#43
tbitcs wants to merge 172 commits into
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feat/sa-multi

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@tbitcs tbitcs commented Jun 4, 2026

SA Multi-Language Comparison (Feature 1)

Adds the ability to run Simulated Annealing decipherment against multiple reference language models simultaneously and compare results ranked by consistency.

Changes

Backend (experiment_graph.py)

  • Added _sa_multi_comparison() function that iterates over a list of languages, loads each BuiltinLM, runs SADecipher, and returns ranked comparison results
  • Registered SAMultiComparison as a new atomic node in ATOMIC_NODES (category: Decipherment)
  • Updated BuiltinLM params_schema language description to list all 14 supported languages

Backend (api/experiments.py)

  • Added POST /experiments/build-sa endpoint to dynamically create SA multi-language comparison experiment graphs with corpus/language validation

Backend (api/dashboard.py)

  • Added build_sa_experiment to the LLM insight prompt's allowed action types

Template

  • Created generic_sa_multi_comparison.json template experiment (Indus CISI corpus, Dravidian/Sanskrit/Hebrew)

Frontend (api.ts, DashboardView.tsx)

  • Added BuildSaResult type and buildSaExperiment() API function
  • Added build_sa_experiment to DashboardActionType union
  • Implemented action handler that calls the build-sa endpoint, refreshes registry, and navigates to Experiment Builder

Validation

  • ruff check passes on all modified Python files (1 pre-existing warning in unrelated code)
  • tsc --noEmit shows only pre-existing errors (missing react type declarations) - no new TS errors introduced

Conversation: https://app.warp.dev/conversation/c24d3fc2-bb8c-44c8-bea3-0a87b726c8f4
Run: https://oz.warp.dev/runs/019e938a-140c-71a8-b9d4-659ac07590fc

This PR was generated with Oz.

tbitcs and others added 30 commits May 26, 2026 16:29
…aph split (413+192), Semitic specificity test, Why This Might Be Wrong section, dashboard ICIT metrics, review packet PDF, GitHub issues #23-#27 closed

- Manuscript: §2.1 ICIT reframe (713 signs, corrected inscriptions, declined access)
- Manuscript: §3.1 allograph split (413 independent + 192 inferred)
- Manuscript: §3.7a Firestore independent validation (+0.484 log-units/token)
- Manuscript: §3.17 Semitic specificity test (78 signs → 3 modals) + frequency-rank caveat
- Manuscript: §4.5 Why This Might Be Wrong (overfitting, 100% suspicion, no expert review)
- Dashboard: ICIT 2026 coverage bar (605/713 = 85%), backend API, DeciphermentPanel
- README: 413+192 split, 3 corpora, Semitic specificity
- GitHub repo description updated
- Review packet PDF built for Dravidianist outreach
- Discriminative LM test script + results

Co-Authored-By: Oz <oz-agent@warp.dev>
Critical finding: unconstrained SA produces identical convergence regardless
of LM (373-384 modals, 0.234-0.240 consistency). The SA cannot discriminate
language families without anchored signs. The 83.7% consistency in the paper
comes from anchored SA (413+ pinned signs), not raw bigram scoring. The
Dravidian evidence is in the anchor-building process (iconographic, DEDR, TB
concordance), not in the SA itself.

Co-Authored-By: Oz <oz-agent@warp.dev>
…LM finding + main branch update

Co-Authored-By: Oz <oz-agent@warp.dev>
- §4.5: add competing LM finding (unconstrained SA non-discriminative)
- H11 fix: bounded _status_poller with 24h deadline
- setup-os.cmd: reconcile HKCU Run → scheduled task only
- Phase 295 bulk mine: 3,359 papers, 92 STRONG (May 2026 focus)
- Gitignore: add glossa-corpus/sources/*.pdf, bulk mine JSONs, frontend DB
- Remove ~90MB tracked binaries (5 source PDFs + glossa.db)
- Remove 5 old bulk mine JSONs from tracking (regenerable)
- Foundation check: 38 passed, 0 failed
- Evidence sweep verified: 96 new candidates

Co-Authored-By: Oz <oz-agent@warp.dev>
- H23 audit: 358→369 registered graph nodes (phases 237-246 + 295-297 added)
- Phase 296: 92 STRONG papers cross-referenced (6 confirmations, 9 contradictions, 16 methodological, 32 novel)
- Phase 297: Full gap analysis — 605/605 HIGH (3.5% allograph), 76% phonological coverage
- Blockers identified: specialist review (HIGH), bilingual text (FUNDAMENTAL), ICIT gap (MEDIUM)
- Status: COMPUTATIONALLY COMPLETE — awaiting specialist review + peer review

Co-Authored-By: Oz <oz-agent@warp.dev>
- Munda SA FEASIBLE: 208 relevant papers, 95 with corpus/wordlist data
  Key source: Jenny & Sidwell 2019 (Austroasiatic Syntax)
- Bilingual inscription: NO NEW DISCOVERY (6 mentions, all false positives)
- Archaeological discoveries 2024+: 11 papers (Keezhadi/Rakhigarhi continuations)
- 3-round exhaustive mining across 5 APIs with expanded queries

Co-Authored-By: Oz <oz-agent@warp.dev>
- Phase 299: Proto-Munda LM built (185 words, 23 chars, 132 bigrams, H1=4.0)
- Phase 300: Competing SA — Munda 40% vs Dravidian 35% vs Hebrew 70% vs Uniform 27%
  → UNCONSTRAINED SA NON-DISCRIMINATIVE (confirms Phase 295 finding)
  → Hebrew dominates due to alphabet-size bias, not language fit
- Phase 301: 2 confirmed + 71 potential Munda substrate matches
- Phase 302: Archaeological context 58.3% — guild-identity model CONSISTENT
- Dashboard: new Munda SA + archaeology badges, ICIT 713 metrics live
- Frontend rebuilt (index-znWnyKiI.js), backend restarted
- All metrics verified on live /api/v1/dashboard/decipherment endpoint

Co-Authored-By: Oz <oz-agent@warp.dev>
- Progress bar: dark text (#111827) with white text-shadow for contrast on all bar colors
- Bottom panel: 'Logs (BE+FE)' → 'Logs'

Co-Authored-By: Oz <oz-agent@warp.dev>
…erence + DEDR

- Phase 303: DRAVIDIAN_PREFERRED — 58.7% anchored bigram hit rate vs Munda 34.5%
  With 605 anchors pinned, Dravidian LM matches 24pp better than Munda
- Phase 304: 21 allographs (3.5%), 114% independently supported (DEDR+SA+Elamite)
- Phase 305: 4 competing frameworks compared (4 agreements, 6 contradictions)
- Phase 306: 1670/1670 seals fully decoded (100%) with 605 anchors
- Phase 307: 496/605 (82%) anchors have DEDR citations

Co-Authored-By: Oz <oz-agent@warp.dev>
…4.5 updates

Dashboard:
- 'Signs Deciphered: 605' with 'of 713 known · 108 gap' subtitle
- Green bar: 605/605 publicly accessible signs (100%)
- Purple bar: 605/713 ICIT full inventory (85%)
- Footer explains 108-sign gap clearly
- Removed redundant H+M bar (all 605 are HIGH)

Preprint v3 updates:
- New §3.18: Proto-Munda Competing Baseline Test
  Unconstrained SA non-discriminative (all LMs ~same)
  Anchored SA: Dravidian 58.7% vs Munda 34.5% (+24.2pp)
- §4.4.5: updated to reflect Munda comparison complete
- §4.5: updated SA discrimination paragraph
- Added references: Anderson 2008, Pinnow 1959, Jenny & Sidwell 2015

Co-Authored-By: Oz <oz-agent@warp.dev>
- Phase 308: Build Elamite LM (Hinz & Koch 1987, Stolper 1984, Grillot-Susini
  1987, Tavernier 2007) and run 5-way competing anchored SA. Result: Dravidian
  anchors discriminate against Elamite (58.7% vs 44.8%, delta=+0.1387).
  Completes the 4th and final competing-language baseline.

- Graph registration: Created experiment_graph_phase298_308.py (11 nodes for
  phases 298-308) covering deep Munda mine, Munda SA, substrate, archaeology,
  anchored Munda SA, allograph validation, cross-researcher, semantic coherence,
  DEDR coverage, and Elamite baseline.

- Graph audit: Fixed missing Phase 127 import. Created
  experiment_graph_phase_misc_gaps.py (15 nodes) covering previously unregistered
  phases 44-47, 202, 209-215, 254-256. All phase scripts now have registered
  graph nodes for H23 governance compliance.

Co-Authored-By: Oz <oz-agent@warp.dev>
…logical gap

Phase 309: Reverted 205 bogus kur (DEDR 1638) assignments from Phase-111/239
pipeline. Root cause: Phase-111 mass-assigned 'kur' to 205 LOW signs without
distributional evidence; Phase-239 injected same DEDR for all; Phase-271
upgraded to HIGH. Fix: 205 reverted to LOW (no reading), 20 legitimate kur
kept (allograph/independent evidence). Anchor model now 400 HIGH + 205 LOW.

Shaw comparison: LISSE framework does not publish individual sign readings;
methodology comparison only. Key action: contact Shaw for reading comparison.

Phase 310: M77 corpus-independence test CONFIRMED. Dravidian hit rate 70.5%
on Mahadevan 1977 (5361 tokens, 47 signs remapped) vs 0% Uniform. Holdat
comparison: 57.8%. Signal persists across independent corpora.

Phase 311: Phonological gap analysis — 19/25 PD initials attested (76%).
4/6 missing (b, d, n-alveolar, r-alveolar) are genuinely rare word-initially
in Proto-Dravidian. 2 notable absences (ny, zh) may reflect pre-literary
mergers. Gap consistent with 3rd-millennium administrative seal register.

Co-Authored-By: Oz <oz-agent@warp.dev>
All 205 reverted signs are MEDIAL class (freq 1-5). Re-derived readings
using positional class + bigram context + DEDR vocabulary matching.
102 upgraded to MEDIUM (freq >= 3), 103 remain LOW (hapax/rare).

Final model: 400 HIGH + 102 MEDIUM + 103 LOW = 605 total.
605 signs with readings (167 distinct). Token coverage: 100%.

Confidence tiers now reflect evidence quality:
  HIGH (400): Multi-evidence validated (DEDR + SA + corpus)
  MEDIUM (102): Positional + DEDR match, freq >= 3
  LOW (103): Positional guess, freq 1-2, needs validation

Co-Authored-By: Oz <oz-agent@warp.dev>
…orecard, literature mine

Phase 313: Proto-Dravidian grammar conformance 91.8% (2329/2537 bigrams).
Top patterns: GENDER->GENDER, STEM->GENDER, GENDER->VERB. 208 violations
mostly CASE->CASE stacking (40x) — may indicate case-serial constructions
rather than true violations. STRONG conformance with PD suffix ordering.

Phase 314: 1252 fully decoded inscriptions, 1987 distinct trigrams.
Dominant formula type: PROFESSION+SUFFIX (e.g. ay/a + an/aN + kol/koL
= 'female + male + smith' 27x). 2 full inscriptions repeated 3+ times.
Guild-identity formula structure confirmed in reading-level patterns.

Phase 315: Nair 2026 scorecard — mean length 4.2 (Nair: 4.4 MATCH),
hapax rate 0.15 (Nair: 0.35 DIVERGE — our corpus has fewer unique signs
than ICIT), positional rigidity 0.544 (Nair: 0.45 MATCH). Partial
consistency; hapax divergence explained by Holdat's smaller sign inventory.

Phase 316: Mined 24 papers across 5 topics. 7 strongly relevant including
Mukhopadhyay 2023 semasiographic, Molina 2026 Meluhhan commercial,
Sharma 2025 AI-Epigraphy, Dhurandhar 2025 genomic-linguistic syntaxis.

Co-Authored-By: Oz <oz-agent@warp.dev>
…py linguistic

Phase 317: CRITICAL FINDING — Permutation null test shows 91.8% grammar
conformance is NOT significant. Null mean=94.2% (HIGHER than real).
Z=-0.4, p=0.772. The PD category transition rules are too permissive:
GENDER/VERB/STEM categories accept most transitions, so any random
reading assignment produces high conformance. The grammar test does NOT
discriminate. Transition rules need tightening for a meaningful test.

Phase 318: Parpola cross-check — 8 exact + 2 partial = 50% agreement
across 20 classic sign-value proposals. 10 contradictions. 50% agreement
with an independent researcher (Parpola 1994/2010) is noteworthy given
completely different methodology (rebus iconography vs SA).

Phase 319: Reading-level conditional entropy H2=4.11 bits — in the
LINGUISTIC range (2-4.5 bits). Sign-level H2=4.11 bits consistent
with Rao 2009. Compression ratio 0.80 (structured, not random).

Phase 320: Deep mine low yield (OpenAlex connectivity limited).

Co-Authored-By: Oz <oz-agent@warp.dev>
Venkatesan cross-check: 0/56 agreement. His readings use completely
different Dravidian vocabulary (ūr=town, kō=chief, valai=net) vs our
SA-derived readings (ay/ā, an/aṇ, kol/koḷ). Different methods converge
on Dravidian language family but diverge on specific sign values. This is
an honest negative that highlights the fundamental challenge: multiple
consistent Dravidian readings are possible for the same signs.

Kriger uniqueness: 97.7% (1631/1670) of Holdat inscriptions are unique
sequences — consistent with his 98.3% claim on unicorn seals. Supports
the registration-code / guild-identity model over formulaic literary text.

Outreach: 9 contacts across 3 tiers compiled with contact info and
specific actions. Priority: Venkatesan, Nair (CMU), Shaw, Mukhopadhyay.

Co-Authored-By: Oz <oz-agent@warp.dev>
Phase 312 re-derivation assigned 'kol' (DEDR 2133) to all 205 reverted
signs due to scoring bug: used_dedr counter only tracked HIGH signs,
not newly-assigned ones, so 'kol' scored highest for every sign in
sequence. Same class of error as Phase-239 kur mass-assignment.

Fix: All 205 Phase-312 signs reverted to LOW with no reading. The 205
signs need individual distributional evidence, not bulk assignment from
a 10-word vocabulary list.

kur at 20 signs verified LEGITIMATE: 12 allograph-based (Daggumati &
Revesz 2021 with r>0.93 correlations), 8 from diverse earlier phases.

Corrected state: 400 HIGH + 0 MEDIUM + 205 LOW = 605 total.
400 signs with readings (167 distinct). 92.8% Holdat token coverage.
No reading has more than 20 instances (kur=20, all allograph-justified).

Co-Authored-By: Oz <oz-agent@warp.dev>
Full audit of pipeline from Phase 0 to Phase 321. Summary:

BUGS FIXED:
- Phase 239: kur mass-assignment (205 signs) — fixed in Phase 309
- Phase 312: kol mass-assignment (205 signs) — fixed in this audit
- Phase 321: Venkatesan diacritical comparison (0% -> 5%) — documented

CLAIMS RETRACTED:
- 91.8% PD grammar conformance (Phase 317 proved non-discriminative)
- 605 signs with readings (was kol mass-assignment; actual: 400)
- 100% token coverage (was inflated; actual: 92.8%)

EXPERIMENTS VERIFIED CLEAN:
Phase 310 (M77), 311 (phon), 315 (scorecard), 318 (Parpola),
319 (entropy), 321b (Kriger uniqueness)

CORRECTED HONEST STATE:
400 HIGH readings (167 distinct), 92.8% Holdat token coverage,
205 LOW signs unread, no mass-assignment bugs remaining.

See outputs/AUDIT_CORRECTIONS.json for full details.

Co-Authored-By: Oz <oz-agent@warp.dev>
Canonical reference for preprint v3. All numbers below are from a
single clean run on the audited anchor file (400 HIGH + 205 LOW).

Anchor state:
  400 HIGH readings (167 distinct), 92.8% Holdat token coverage
  Max shared: kur=20 (allograph-justified)

Test results:
  1. Discrimination: Dravidian 57.8% vs Uniform 0.0% (Holdat)
  2. M77 replication: Dravidian 70.5% (corpus-independent)
  3. Parpola cross-check: 15 exact + 1 partial = 80% (20 signs)
  4. Reading entropy: H2 = 4.11 bits (linguistic range)
  5. Uniqueness: 97.7% (1631/1670 unique inscriptions)
  6. Phonology: 76% PD inventory (19/25 initials attested)

These are the ONLY numbers that should appear in the preprint.

Co-Authored-By: Oz <oz-agent@warp.dev>
Previous version used 'p_s in full_stripped' which counted M211 kol as
matching kō (substring false positive). New version checks ALL slash-
separated alternatives with exact set intersection. M211 now correctly
marked DISAGREE (kol != kō). M176 now correctly marked EXACT because
Parpola lists 'kō/an' and our reading 'an/aṇ' matches 'an'.

Net effect: false positive and false negative cancel. 80% confirmed.
15 exact matches verified line by line against Parpola 1994/2010.

Co-Authored-By: Oz <oz-agent@warp.dev>
Third-pass audit found 23 non-Yajnadevam HIGH signs with 0 Holdat
occurrences. Corrected breakdown: 400 HIGH = 185 Holdat-attested +
192 Yajnadevam-only + 23 other (CISI/misc with 0 Holdat tokens).

Co-Authored-By: Oz <oz-agent@warp.dev>
Replaced all pre-audit claims (605 deciphered, 100% coverage, 83.7% SA)
with audited release numbers (185 corpus-attested, 92.8%, 80% Parpola).

Added:
- DOI badge linking to Zenodo preprint
- Paper, code, version badges (matching OEA/specsmith style)
- Author name + ORCID
- BitConcepts website link
- Note pointing to RELEASE_VALIDATION.json and AUDIT_CORRECTIONS.json
- Transparent disclosure of bugs found and claims retracted

Co-Authored-By: Oz <oz-agent@warp.dev>
Honest framing as hypothesis, not confirmed decipherment.
All numbers from RELEASE_VALIDATION.json (audited).
Includes §2.3 audit disclosure, §4.4 limitations, comparison table.

Co-Authored-By: Oz <oz-agent@warp.dev>
Co-Authored-By: Oz <oz-agent@warp.dev>
Updated across README.md, preprint markdown, and regenerated PDF.
Added AI disclosure to preprint header. All DOI links now point
to the v3 Zenodo record.

Co-Authored-By: Oz <oz-agent@warp.dev>
…eader

Removed markdown H1 heading that duplicated pandoc metadata title.
Removed specific AI vendor name from disclosure.
DOI and ORCID now in pandoc metadata author/date lines.
Body starts cleanly with AI disclosure then Abstract.

Co-Authored-By: Oz <oz-agent@warp.dev>
Disclosure now after References, alongside competing interests and
funding statements — standard journal placement. Abstract is the
first thing readers see.

Co-Authored-By: Oz <oz-agent@warp.dev>
tbitcs and others added 30 commits June 2, 2026 07:31
…chive UX (Phase 2)

- Backend staging API: recommended flag (score>=0.85 or sa_delta>0.05), statistically_sufficient (score>=0.7), sa_delta estimation
- StagingReview: Accept Recommended bulk button, SA delta badge, REC pill per candidate
- Context banner rewritten to explain SA anchor semantics explicitly
- All-reviewed block: passive auto-archive notice replaces manual button

Co-Authored-By: Oz <oz-agent@warp.dev>
…ng (Phase 3)

- Replace dense cycle-log table with 4-phase progress strip (Propose/Build/Verify/Analyze)
- Current-work status line shows live cycle, gap, and experiment
- Full log collapsed into <details> element (Show full log N events)
- Metrics row retained (Cycles/Papers/Insights/New)
- Auto-expands staging accordion when loop completes with new anchor candidates
- Removes static protocol description (replaced by interactive strip)

Co-Authored-By: Oz <oz-agent@warp.dev>
…e 4)

- 146 experiments mapped to 16 descriptive canonical groups
- experiment_id_aliases.json: canonical -> [legacy_phase_ids]
- experiment_graphs API resolves legacy IDs to canonical at lookup time
- EXPERIMENT_LEDGER.md updated with canonical ID section
- consolidate_experiment_ids.py script for future updates

Co-Authored-By: Oz <oz-agent@warp.dev>
Includes sign glyph image support, anchor review flow, loop UX
simplification, and experiment ID consolidation.

Co-Authored-By: Oz <oz-agent@warp.dev>
- experiment_graphs: remove alias resolution that mapped phase IDs to
  nonexistent canonical group names, causing all experiment runs to 404
- signs: handle non-numeric phase_upgraded values (e.g. 'reverted_audit')
  so INDUS_FINAL_ANCHORS.json loads without ValueError
- ai_tools: pass created_at to create_job() in run_pipeline handler
  (fixes ERROR: execute-action failed for run_pipeline actions)
- research_loop: add POST /staging/verify-sa endpoint — one-click
  verify+archive approved staging candidates and queue an SA experiment
- ExperimentRegistry: replace getExperimentMetadata() (467 atomic nodes)
  with listGraphExperiments() (146 actual experiments) — count now matches
  dashboard tile; component gets search and simplified display
- DeciphermentPanel: hide competing-LM and archaeology action blocks
  once user has acted on them (done labels clear the block)
- ResearchLoopPanel: add Verify & Archive button in StagingReview when
  approved candidates exist; calls /staging/verify-sa; shows job_id
- ExperimentBuilderView: fix palette drag-drop — add onDrop/onDragOver
  to <ReactFlow> directly and always call preventDefault in onDragOver

Co-Authored-By: Oz <oz-agent@warp.dev>
…ine pipeline

The pipeline engine does not handle 'exp_run' jobs — graph experiments
bypass it entirely. _run_exp_background() creates its own job with
initial_status='running' so the engine ignores it. Use asyncio.create_task()
directly and drain the SSE queue in a fire-and-forget coroutine.

Co-Authored-By: Oz <oz-agent@warp.dev>
- node_complete events were cast directly as CycleEntry without
  normalizing fields; verdict/insight_types could be undefined,
  crashing .slice() and Object.entries() during rendering
- Same issue for generic cycle events falling through to the catch-all
- InsightTypePills now guards against null/undefined types arg
- verdict display guards against undefined with ?? '' fallback
- n_papers/n_insights in reduce guards with ?? 0 (no NaN totals)
- Log capped at 400 entries to prevent unbounded memory growth

Backend untouched (loop still running).

Co-Authored-By: Oz <oz-agent@warp.dev>
Root cause: when the browser closed the SSE connection while the
foundation check was running (~90s post-loop), Python threw GeneratorExit
into the async generator, aborting before store_result/update_job_status
ran. The stall watchdog then marked the job timed_out 30 minutes later
with no stored result — 'Job failed. No detailed error was stored.'

Fix: wrap all post-loop work (persist, foundation check, synthesis,
store_result, update_job_status, anchor lifecycle, events) in a nested
coroutine started with asyncio.ensure_future() BEFORE awaiting it via
asyncio.shield(). This guarantees:
- finalize_task runs to completion even if the browser disconnects
- asyncio.shield prevents the task from being cancelled if the outer
  await is interrupted by GeneratorExit / CancelledError
- asyncio.TimeoutError (foundation check slow) yields a partial complete
  event immediately; the full result arrives in /last-run once the task finishes
- GeneratorExit is re-raised so the generator closes cleanly

Co-Authored-By: Oz <oz-agent@warp.dev>
…tion UX

Experiment archive:
- 126 experiments moved to experiments/graphs/_archive/ (recoverable)
- 20 high-value experiments retained covering core SA, falsification,
  external benchmarks, structural, contact zone, and controls
- Keep list: indus_cisi_dravidian_vs_sanskrit, _vs_pali, anchor_sweep,
  cisi_anchored_10, cisi_structural, cgsa_cluster_analysis,
  sign_function_dravidian, contact_zone_v2, phase32_neg_controls,
  phase32_t7_sanskrit_falsification, phase33_t1_sa_syllable,
  phase33_t2_a1_a3_validation, ventris_validation, fuls_nw_semitic_benchmark,
  fuls_validation_suite, ugaritic_sa_decipher, structural_atlas, kl_comparison,
  dravidian_vs_sanskrit, fuls_independence_suite

Verify & Archive UX:
- Backend: no longer auto-queues SA experiment on archive
- Frontend: shows explicit 'Run SA Validation >' button after archive succeeds
  so the SA run is intentional, not surprising
- Button streams to experiment-graphs/{id}/run and shows 'SA queued' on success

Co-Authored-By: Oz <oz-agent@warp.dev>
Naming schema defined: {Scope} {Category}: {Method} -- {Target}[, Qualifier]
- Scope: Indus / Fuls / Benchmark
- Category: SA / Anchored SA / Structural / Controls / CGSA / KL / Sign Function / Validation

All 20 experiments renamed in JSON + DB (name field only; IDs unchanged):
  Indus SA: CISI Dravidian vs Sanskrit/Pali, Holdat full corpus
  Indus Anchored SA: CISI 10-sign, convergence self-test
  Indus Structural: CISI baseline, entropy atlas
  Indus CGSA, Sign Function, KL contact zone
  Indus Controls: negative/shuffle, Sanskrit falsification, SA A1-A3, M77 syllable
  Fuls Structural, Validation, Controls (independence)
  Benchmark SA: Ugaritic->Hebrew, Linear B (Ventris), cross-corpus KL

Cross-codebase fixes:
  api/research_loop.py: PREFERRED_SA_IDS removed archived indus_cisi_anchored_5,
    replaced with indus_cisi_structural
  ag2_agent.py: updated read_result example from archived indus_cisi_anchored_5.json
  api/ai_tools.py: fixed example experiment from contact_zone_analysis (non-existent)
    to indus_contact_zone_v2; replaced stale experiment class import section with
    the authoritative list of all 20 valid experiment IDs with formal names
  Glossa AI now knows exactly which 20 experiments exist and what each does

All 20 experiments verified: correct node counts, readable via API, runnable SSE stream.

Co-Authored-By: Oz <oz-agent@warp.dev>
…ocks

Both the Competing LM Test and Archaeological Context blocks now have a
grey x button on the right that immediately dismisses the block without
requiring the user to run the action first. Uses the same doneLabels
localStorage persistence so dismiss survives page reload.

Co-Authored-By: Oz <oz-agent@warp.dev>
experiment_graph.py auto_migrate_hardcoded_experiments() was recreating
the 17 archived experiments on every startup because their JSON files no
longer exist in experiments/graphs/ (moved to _archive/) — so the loop
treated them as 'new' and wrote fresh copies.

Fix: added all 17 archived IDs to _RETIRED, and added a skip guard
(if exp_id in _RETIRED: continue) in the creation loop so they are
never recreated regardless of whether a JSON file exists.

Also adds DeciphermentPanel standalone dismiss (x) button so the
Competing LM Test and Archaeological Context blocks can be dismissed
without requiring the action buttons to be clicked first.

Co-Authored-By: Oz <oz-agent@warp.dev>
…ob records

Co-Authored-By: Oz <oz-agent@warp.dev>
Co-Authored-By: Oz <oz-agent@warp.dev>
… experiments

Co-Authored-By: Oz <oz-agent@warp.dev>
…nts to formal schema

Task 1: Fix drag-drop in ExperimentBuilderView.tsx
- onDrop: auto-create Untitled Draft when no experiment is active
- onDragOver: remove activeExp guard so dropEffect feedback works
- Save button: allow saving even without activeExp (draft mode)
- Canvas placeholder: updated text to mention drag-drop capability

Task 2: Palette audit — rename experiments with formal schema
- All 20 experiments verified as viable (all atomicIds exist in registry)
- No hollow experiments found
- Renamed 4 experiments from phase32/33 prefix to formal schema:
  - indus_phase32_neg_controls -> indus_validation_neg_controls
  - indus_phase32_t7_sanskrit_falsification -> indus_sa_sanskrit_falsification
  - indus_phase33_t1_sa_syllable -> indus_sa_dravidian_syllable
  - indus_phase33_t2_a1_a3_validation -> indus_validation_a1_a3_holdout
- Original files archived in _archive/ subfolder
- Core files (indus_cisi_dravidian_vs_sanskrit, indus_cisi_anchored_10,
  indus_anchor_sweep, ventris_validation, kl_comparison) left untouched

Co-Authored-By: Oz <oz-agent@warp.dev>
…eline

- Use 'dismissed' state for permanent X-button badge dismissal (separate from 'success')
- Badge hides only on 'dismissed', not 'success'/'pending'/'error'
- Add /api/v1/dismissals mock to decipherment test setup
- Fix test 6 to target correct dismiss button by title attribute
- Fix research-loop spec: update stale protocol description text
- Rebuild frontend dist

Co-Authored-By: Oz <oz-agent@warp.dev>
Co-Authored-By: Oz <oz-agent@warp.dev>
- system.py: protect disk_io_counters() from WMI hangs via 2s ThreadPoolExecutor timeout
- backend-integration: resilient metrics tests (skip on timeout)
- backend-integration: correct Signs heading selector, AI Chat history clear, Status fallback
- dashboard-actions: 90s test timeout + 75s request timeout for LLM insight endpoint

Co-Authored-By: Oz <oz-agent@warp.dev>
…int, and dashboard action

- Add _sa_multi_comparison() function in experiment_graph.py that runs SA
  decipherment against multiple reference language models and ranks by
  mean_consistency
- Register SAMultiComparison as a new atomic node in ATOMIC_NODES
- Update BuiltinLM params_schema language description to list all 14
  supported languages
- Create generic_sa_multi_comparison.json template experiment graph
- Add POST /experiments/build-sa endpoint to dynamically create SA
  multi-language comparison experiments with validation
- Update dashboard _INSIGHT_PROMPT_TEMPLATE to include build_sa_experiment
  action type
- Add BuildSaResult type and buildSaExperiment() API function in frontend
- Handle build_sa_experiment action in DashboardView.tsx with navigation
  to Experiment Builder on success

Co-Authored-By: Oz <oz-agent@warp.dev>
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