Reconcile draft 924 with the confirmed current-main conflict before release

[realmarcin]

Draft #924 at fc7a4645911fe539f84f585e7b83fbf699c2ace8 has a confirmed conflict against the one captured actual remote main d227d23913ff3d99e2a369e79a2194e80601d71e. A disposable Git object-store merge-tree --write-tree returns exit1 with 619 conflict paths, all generated pages/*.html. GitHub reports dirty/CONFLICTING and has created no required check runs. Both PR APIs still report the older base 91441a298a757fe276caab644c7120a7657a9bb5; the actual main identity comes from the simultaneously captured git ls-remote result and the immutable fetched object, rather than trusting that stale PR field.

The validated branch contains605-trait common/paired-graph maps, a complete independently reviewed site, passing just qc, all1,518 tests and the accepted runtime440 correction with44 focused tests. The new main adds exactly two traits:

• traitmech:000211: DISARM system, data/traits/genomics/disarm_system.yaml.
• traitmech:000212: CBASS system, data/traits/genomics/cbass_system.yaml.

The reconciled total is607. All605 existing semantic rows and their parent labels are unchanged, so at most two new common-cache keys are needed. No graph producer, adapter or runtime changed. Incoming proposal/history/report updates, two curation scripts and one audit test must be preserved. There are no source conflicts.

Prepare a guarded source merge against this exact main, preserve the619 generated conflicts until genuinely refreshed output exists, export the complete607-row snapshot, back up/reuse the verified cache into a fresh build and generate the current common map. Refresh both specialty layouts with the existing source/aliases and actual parser receipts; retain direct/proxy labels and original artifacts/receipts. Render through the maintained rendering-only path, validate every current route, then resolve only verified generated files and run required gates. No stale side selection, force push, remote merge or repeated speculative main chasing is authorized by this tracker.

Acceptance: the607 source and map receipts are current, independent artifact/site review passes, all619 generated conflicts are replaced by verified output, and required GitHub checks run and pass on the updated draft.

Related #927 and #929 implement publication freshness and paired generation; they do not track this newly observed release-refresh boundary. The open-issue search for924 found only those two. Evidence: runtime440-transition-graph-pair/trait-conflict/inspection.json, complete merge-tree.stdout, and traitmech/publication/conflict-remote-refs.txt. Inspection read existing605 JSONL labels plus only the two added YAML blobs; no model, vector-cache scan, full graph-source read or prepared-tree mutation occurred.

[realmarcin]

The accepted 607-record refresh and #944 browser disclosure fix are now in draft #924 at e4807b2e3b4e2d03f8d1d9dd35c34e7700e5c354. Independent source/common-vector/paired-graph/site reviews passed, as did maintained just qc, all 1,522 tests, and all 16 governed artifact checks.

GitHub subsequently reports the updated draft as CONFLICTING. Its PR API still reports base d227d23913ff3d99e2a369e79a2194e80601d71e, but the actual refs/heads/main captured once is now 7b33697048ccad04b50a052696e29d4993c7332e.

Exact disposable merge-tree reproduction returns 621 conflicts, all generated pages/*.html. The incoming source delta adds one trait, data/traits/genomics/phosphorothioate_defense_system.yaml (traitmech:000213), bringing the corpus to 608. All 607 existing source blobs are identical; the actual semantic adapter gives the new row text SHA256 0f36b6ad3c6d94f90de25ab258e0484f34a8c2b500a790eb313ee96fbeaf6b9d. An ignored-inclusive source search confirms no existing record references the newly introduced identifier, so its new label does not change an existing parent-label feature.

There are 637 incoming paths, predominantly maintained generated pages. The only executable-source delta is the upstream additive scripts/add_phosphorothioate_defense_system_trait.py and a corresponding existing audit-test adjustment; the map adapters, renderers/templates (including #944), vector runtime, graph producers, alias inputs and dependency locks are unchanged. Proposal/history/report updates will be preserved as exact incoming blobs.

This remains the same source-currentness blocker tracked here. The bounded follow-up will use this single frozen main identity, reuse 607 verified vectors and encode only the one confirmed new semantic key, refresh paired graph receipts for the 608-record raw corpus, then regenerate/review the site. The just-completed full QA remains evidence for unchanged code; only affected current-corpus/publication/new-record checks and required final-head GitHub CI will be repeated. No prepared source/model/graph/site changes have begun for this follow-up; no further speculative main fetch is planned.

[realmarcin]

The 608-record refresh is complete and independently reviewed at draft head 3b32d6a1e5edc555a0ced92eae44513c3c43baff, including all map/site artifacts and six affected validation gates (62 tests).

The remaining conflict is now bound to exact current main 86021eebbba77b990a8668c53a01ab25f978937b, whose parent is the prior captured 7b33697048ccad04b50a052696e29d4993c7332e. GitHub's PR base fields still reported the older parent; the branch-ref API exposed the missed commit. No CI runs started for the conflicted draft head.

Read-only inspection in a disposable object store confirms all 608 existing trait YAML blobs are unchanged and exactly one record is added: traitmech:000214, abortive infection system. Its actual adapter text SHA256 is 1baf1fc0827056ff5e2e5cb4bfd68defbd02210b6c45ed22020f905b757c782d; an ignored-inclusive source search found no earlier references to that new identifier. The immutable merge has 622 conflicts, all generated HTML. The reviewed graph/adapter/runtime implementations remain unchanged; incoming maintenance files are separately bound to main.

The bounded follow-up will export the exact 609-record corpus, reuse the 608-record semantic cache with only the approved new key, refresh the paired graph receipts and maintained site, and run affected source/publication/history checks. Prior artifacts, caches, independent reviews and full QA remain preserved. No later-main refresh or remote merge is included.

[realmarcin]

The final source boundary is frozen at 170463d6f1b5e3faa0e1d3b4e3bf7b3c64389dce, from the accepted and published 609-trait integration 0c856d96a1a7e175e337a59b4fbefb63549c64e1. This is the same source-refresh issue; no additional main lookup is planned during this refresh.

The disposable merge inspection identifies 611 source records: all 609 existing YAML blobs and modes remain identical, with only traitmech:000215 (Gabija system, #946) and traitmech:000216 (Thoeris system, #948) added. The unchanged semantic adapter yields exactly two new keys. The automatic merge has 623 generated-HTML-only conflicts and 646 incoming changed paths.

The source plan preserves all 19 incoming auxiliary bindings, including both new one-off writers, the modified tests/test_audit_graph_protein_taxa.py, proposal skill, history, proposals and reports. It also preserves 455 implementation bindings, all 29 existing map artifacts/generations, the 609-input/cache evidence, runtime 9ef77083 and released fleet pin c8b8f89e.

Independent source-plan review and actual source/export acceptance precede dependent numerical work. Planned later validation includes both added-record checks, the incoming modified audit-test module, current publication/history/fresh-render checks and final-head GitHub CI. Existing broad QA is retained for unchanged implementation; one-off curation writers will be preserved without being executed. No workflow, queue or other curation process is changed.