Correct TAC filament topology and cytoskeleton parthood

[realmarcin]

Summary

Closes #2284. Closes #2285.

Correct the tripartite attachment complex record after a whole-record scientific review:

• Exclusion-zone filaments occupy the cytoplasmic basal-body/outer-membrane region; unilateral filaments bridge inner membrane to kDNA.
• Correct the four spatial graph links and make the nonmechanistic scope visible.
• Represent cytoskeleton as part_of, not an is-a parent.

Exact GO identity, PROPOSED status, all three protein claims, UNKNOWN essentialities, taxa, old histories and the #769 fixes are preserved. One append-only EDIT accompanies the guarded native write. One semantic embedding was re-encoded offline through the native pinned model helper; 908 other vectors are unchanged. Derived PCA/neighbor files and site copies are regenerated, accounting for the larger generated diff.

Review Lineage

• Observation: reviews/structured/20261012T045744Z-tac-filament-topology-and-parthood/review.yaml and review.md (F1/F2).
• Resolution: reviews/structured/20261012T052500Z-tac-topology-and-parthood-resolved/review.yaml and review.md.
• Stable keys: tac-filament-compartment-reversal, tac-cytoskeleton-is-a-versus-part-of.

Same-agent review and curation, not independent human sign-off. Ogbadoyi Methods/Results/Discussion and Figures2/6, TAC40 Results/Discussion/Methods, TAC102 relevant Results/Discussion/Methods and its republication notice were inspected. Zhao reading was limited to the complete primary abstract and early full-page localization/RNAi Results before an access challenge. Full limitations are in the immutable bundles. No raw-data reanalysis or new measurement.

Verification

• Fresh full local QC: 987 passed, 3 skipped in 810.43s (0:13:30); 909 strict records and 1724 histories.
• Direct target schema/strict/snippet checks, live global authority/trait checks, canonical archive and patch-preservation assertions passed.
• The original observation, all older bundles and all 62 pre-existing untracked reports are unchanged.
• The three other source-gathering targets remain pending, not counted as complete.
• Require all four PR and all four native merge-group gates; no bypass.

[realmarcin]

Adversarial Review

Same-agent review of the exact PR head, not an independent reviewer or human scientific sign-off.

No additional actionable findings. The two pre-curation major findings are tracked in #2284 and #2285 and have explicit immutable successor dispositions.

Checks applied:

• Challenged the compartment assignment against the defining Ogbadoyi Results, Methods and Discussion and inspected Figure 2 ultrastructure and Figure 6 schematic. Exclusion-zone filaments are cytoplasmic; unilateral filaments connect inner membrane to kDNA. The corrected four-link chain matches those distinct regions.
• Checked that this did not become a temporal assembly or protein-level force-transfer claim. The native NONMECHANISTIC classification and displayed spatial-linkage caveat remain explicit. The last two graph edges, node identifiers and component references are preserved.
• Checked GO relation direction against the live cytoskeleton child relation and the local schema contract. The change is part_of, not a reversed edge or a guessed new is-a parent. Exact GO:0120121 identity is unchanged.
• Compared the entire corrected YAML with the pre-curation record. Protein roles, UNKNOWN assembly essentialities, label-only groundings, taxonomic scope, canonical example, function, discussion, PROPOSED status and earlier #769 fixes are preserved.
• Verified generated HTML exposes both corrected compartments, the proper edge endpoints and Part of relation. No generated page was manually edited.
• Audited the larger generated diff: exactly one record embedding was re-encoded offline with the repository's pinned model/helper; the other 908 vector records and model metadata are unchanged. PCA and neighbor outputs, including site copies, were regenerated and passed native drift checks.
• Verified append-only inline/repository EDIT history, unchanged predecessor review, exact F1/F2 resolution lineage and preservation of all older bundles and 62 pre-existing untracked reports. Only the scoped 12 publication paths are staged/committed.
• Fresh full native QC, direct record checks, authority/trait checks, immutable archive checks and targeted preservation assertions passed. Required PR and native merge-group gates remain mandatory; this review does not waive them.

Limits: Zhao was read at complete primary abstract plus early full-page localization/RNAi Results scope before a challenge, not complete Methods. No raw image reanalysis or new quantitative measurement. Other pending source-gathering records are not counted complete by this PR.