fix(ci): restore topology classification and Admitted workflow extraction

[gHashTag]

Closes #3574

Summary

• Classify gate-topology.yml and untrusted-input-gate.yml as merge-critical in the topology checker. Lower the unclassified ceiling from 27 to 26; do not relax it or change GitHub branch protection.
• Replace the Admitted harness's formatting-sensitive regex with structural YAML extraction of the unique named Bash step in jobs.build.steps.
• Run the extracted body with GitHub's strict Bash flags and retain the existing clean, Admitted, missing-file, expanded-population, and empty-population controls.
• Add topology and extraction regression controls, install PyYAML explicitly in Untrusted Input Gate, and record the change in docs/now/.

Validation

• Gate Topology: all local workflow check commands pass, including topology self-tests and FPGA claim-depth positive/negative controls.
• Untrusted Input Gate: all 11 local workflow check steps pass.
• git diff --check passes.
• Hosted CI will be checked after opening this PR; local success is not a claim of hosted CI success.

Scope and risk

This repairs two existing master failures, not Trinity Memory behavior. No changes to the production Coq step, proofs, compiler, specifications, or branch protection. The 26 remaining unclassified workflows and broader Coq coverage debt remain outside this PR.

The harness now depends on PyYAML, explicitly installed by its workflow. This PR is to remain unmerged pending approval.

[github-actions]

📓 NotebookLM Notebook linked to this PR

• Notebook ID: b83263109fb055dc
• URL: https://notebooklm.google.com/notebook/b83263109fb055dc

This notebook contains session context, decisions, and artifacts for this work.

[github-actions]

PR Dashboard

Generated at: 2026-09-12 03:12:49 UTC

• fix(ci): restore topology classification and Admitted workflow extraction #3575 fix(ci): restore topology classification and Admitted workflow extraction | Created: 2026-09-12 | Updated: 2026-09-12 | 21 failing / 30 total
• fix(ci): make the JSON gate strict, and make the one file it refuses legal #3395 fix(ci): make the JSON gate strict, and make the one file it refuses legal | Created: 2026-09-07 | Updated: 2026-09-07 | 0 failing / 30 total
• fix(rust): a function type is a type alias, not a const's value #3365 fix(rust): a function type is a type alias, not a const's value | Created: 2026-09-06 | Updated: 2026-09-06 | 0 failing / 38 total
• coq(CorePhi): replace proofs that were never checked by a compiler #3343 coq(CorePhi): replace proofs that were never checked by a compiler | Created: 2026-09-06 | Updated: 2026-09-06 | 5 failing / 32 total
• ci(coq): report all thirteen files instead of stopping at the first error #3342 ci(coq): report all thirteen files instead of stopping at the first error | Created: 2026-09-06 | Updated: 2026-09-06 | 3 failing / 30 total
• skill: spool four lessons from this pass #3327 skill: spool four lessons from this pass | Created: 2026-09-05 | Updated: 2026-09-05 | 1 failing / 28 total
• chore(ci)(deps): bump actions/attest-build-provenance from 1 to 4 #3001 chore(ci)(deps): bump actions/attest-build-provenance from 1 to 4 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 31 total
• chore(ci)(deps): bump softprops/action-gh-release from 2 to 3 #3000 chore(ci)(deps): bump softprops/action-gh-release from 2 to 3 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 31 total
• chore(ci)(deps): bump github/codeql-action from 3 to 4 #2999 chore(ci)(deps): bump github/codeql-action from 3 to 4 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 29 total
• Land the formal verification harness on master (it has never run) #2727 Land the formal verification harness on master (it has never run) | Created: 2026-08-27 | Updated: 2026-09-05 | 5 failing / 24 total
• chore(deps)(deps): bump thiserror from 2.0.18 to 2.0.20 #2693 chore(deps)(deps): bump thiserror from 2.0.18 to 2.0.20 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump hyper from 1.10.1 to 1.11.0 #2692 chore(deps)(deps): bump hyper from 1.10.1 to 1.11.0 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 33 total
• chore(deps)(deps): bump base64 from 0.22.1 to 0.23.1 #2691 chore(deps)(deps): bump base64 from 0.22.1 to 0.23.1 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump serde from 1.0.228 to 1.0.229 #2690 chore(deps)(deps): bump serde from 1.0.228 to 1.0.229 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump uuid from 1.23.2 to 1.25.0 #2689 chore(deps)(deps): bump uuid from 1.23.2 to 1.25.0 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• Unbreak FPGA CI and correct two unbacked hardware claims #2081 Unbreak FPGA CI and correct two unbacked hardware claims | Created: 2026-08-11 | Updated: 2026-08-20 | 5 failing / 27 total

Summary

Status	Count
Total Open PRs	16
PRs with Failing Checks	13
PRs with All Checks Green	3
READY	2
FAILING	13
PENDING	0
NO CHECKS YET	0

These columns do not partition: 2 + 13 + 0 + 0 = 15, and there are 16 open PRs. A PR is being counted twice or not at all.

Seal Status

• ⚠️ STALE -- sha256(compiler.rs)=d4c5b22b471e != manifest seal=87e5cbd3ad94.
  The committed NMSE numbers were certified against an older compiler.rs.
  Run scripts/reseal-check.sh locally for the two-step reseal command (advisory; not a merge gate).

[github-actions]

📓 NotebookLM Notebook linked to this PR

• Notebook ID: b83263109fb055dc
• URL: https://notebooklm.google.com/notebook/b83263109fb055dc

This notebook contains session context, decisions, and artifacts for this work.

[github-actions]

PR Dashboard

Generated at: 2026-09-12 03:14:27 UTC

• fix(ci): restore topology classification and Admitted workflow extraction #3575 fix(ci): restore topology classification and Admitted workflow extraction | Created: 2026-09-12 | Updated: 2026-09-12 | 15 failing / 31 total
• fix(ci): make the JSON gate strict, and make the one file it refuses legal #3395 fix(ci): make the JSON gate strict, and make the one file it refuses legal | Created: 2026-09-07 | Updated: 2026-09-07 | 0 failing / 30 total
• fix(rust): a function type is a type alias, not a const's value #3365 fix(rust): a function type is a type alias, not a const's value | Created: 2026-09-06 | Updated: 2026-09-06 | 0 failing / 38 total
• coq(CorePhi): replace proofs that were never checked by a compiler #3343 coq(CorePhi): replace proofs that were never checked by a compiler | Created: 2026-09-06 | Updated: 2026-09-06 | 5 failing / 32 total
• ci(coq): report all thirteen files instead of stopping at the first error #3342 ci(coq): report all thirteen files instead of stopping at the first error | Created: 2026-09-06 | Updated: 2026-09-06 | 3 failing / 30 total
• skill: spool four lessons from this pass #3327 skill: spool four lessons from this pass | Created: 2026-09-05 | Updated: 2026-09-05 | 1 failing / 28 total
• chore(ci)(deps): bump actions/attest-build-provenance from 1 to 4 #3001 chore(ci)(deps): bump actions/attest-build-provenance from 1 to 4 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 31 total
• chore(ci)(deps): bump softprops/action-gh-release from 2 to 3 #3000 chore(ci)(deps): bump softprops/action-gh-release from 2 to 3 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 31 total
• chore(ci)(deps): bump github/codeql-action from 3 to 4 #2999 chore(ci)(deps): bump github/codeql-action from 3 to 4 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 29 total
• Land the formal verification harness on master (it has never run) #2727 Land the formal verification harness on master (it has never run) | Created: 2026-08-27 | Updated: 2026-09-05 | 5 failing / 24 total
• chore(deps)(deps): bump thiserror from 2.0.18 to 2.0.20 #2693 chore(deps)(deps): bump thiserror from 2.0.18 to 2.0.20 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump hyper from 1.10.1 to 1.11.0 #2692 chore(deps)(deps): bump hyper from 1.10.1 to 1.11.0 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 33 total
• chore(deps)(deps): bump base64 from 0.22.1 to 0.23.1 #2691 chore(deps)(deps): bump base64 from 0.22.1 to 0.23.1 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump serde from 1.0.228 to 1.0.229 #2690 chore(deps)(deps): bump serde from 1.0.228 to 1.0.229 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump uuid from 1.23.2 to 1.25.0 #2689 chore(deps)(deps): bump uuid from 1.23.2 to 1.25.0 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• Unbreak FPGA CI and correct two unbacked hardware claims #2081 Unbreak FPGA CI and correct two unbacked hardware claims | Created: 2026-08-11 | Updated: 2026-08-20 | 5 failing / 27 total

Summary

Status	Count
Total Open PRs	16
PRs with Failing Checks	13
PRs with All Checks Green	3
READY	2
FAILING	13
PENDING	0
NO CHECKS YET	0

These columns do not partition: 2 + 13 + 0 + 0 = 15, and there are 16 open PRs. A PR is being counted twice or not at all.

Seal Status

• ⚠️ STALE -- sha256(compiler.rs)=d4c5b22b471e != manifest seal=87e5cbd3ad94.
  The committed NMSE numbers were certified against an older compiler.rs.
  Run scripts/reseal-check.sh locally for the two-step reseal command (advisory; not a merge gate).

[github-actions]

📓 NotebookLM Notebook linked to this PR

• Notebook ID: b83263109fb055dc
• URL: https://notebooklm.google.com/notebook/b83263109fb055dc

This notebook contains session context, decisions, and artifacts for this work.

[github-actions]

PR Dashboard

Generated at: 2026-09-12 03:17:16 UTC

• fix(ci): restore topology classification and Admitted workflow extraction #3575 fix(ci): restore topology classification and Admitted workflow extraction | Created: 2026-09-12 | Updated: 2026-09-12 | 20 failing / 27 total
• fix(ci): make the JSON gate strict, and make the one file it refuses legal #3395 fix(ci): make the JSON gate strict, and make the one file it refuses legal | Created: 2026-09-07 | Updated: 2026-09-07 | 0 failing / 30 total
• fix(rust): a function type is a type alias, not a const's value #3365 fix(rust): a function type is a type alias, not a const's value | Created: 2026-09-06 | Updated: 2026-09-06 | 0 failing / 38 total
• coq(CorePhi): replace proofs that were never checked by a compiler #3343 coq(CorePhi): replace proofs that were never checked by a compiler | Created: 2026-09-06 | Updated: 2026-09-06 | 5 failing / 32 total
• ci(coq): report all thirteen files instead of stopping at the first error #3342 ci(coq): report all thirteen files instead of stopping at the first error | Created: 2026-09-06 | Updated: 2026-09-06 | 3 failing / 30 total
• skill: spool four lessons from this pass #3327 skill: spool four lessons from this pass | Created: 2026-09-05 | Updated: 2026-09-05 | 1 failing / 28 total
• chore(ci)(deps): bump actions/attest-build-provenance from 1 to 4 #3001 chore(ci)(deps): bump actions/attest-build-provenance from 1 to 4 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 31 total
• chore(ci)(deps): bump softprops/action-gh-release from 2 to 3 #3000 chore(ci)(deps): bump softprops/action-gh-release from 2 to 3 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 31 total
• chore(ci)(deps): bump github/codeql-action from 3 to 4 #2999 chore(ci)(deps): bump github/codeql-action from 3 to 4 | Created: 2026-09-01 | Updated: 2026-09-07 | 2 failing / 29 total
• Land the formal verification harness on master (it has never run) #2727 Land the formal verification harness on master (it has never run) | Created: 2026-08-27 | Updated: 2026-09-05 | 5 failing / 24 total
• chore(deps)(deps): bump thiserror from 2.0.18 to 2.0.20 #2693 chore(deps)(deps): bump thiserror from 2.0.18 to 2.0.20 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump hyper from 1.10.1 to 1.11.0 #2692 chore(deps)(deps): bump hyper from 1.10.1 to 1.11.0 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 33 total
• chore(deps)(deps): bump base64 from 0.22.1 to 0.23.1 #2691 chore(deps)(deps): bump base64 from 0.22.1 to 0.23.1 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump serde from 1.0.228 to 1.0.229 #2690 chore(deps)(deps): bump serde from 1.0.228 to 1.0.229 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• chore(deps)(deps): bump uuid from 1.23.2 to 1.25.0 #2689 chore(deps)(deps): bump uuid from 1.23.2 to 1.25.0 | Created: 2026-08-24 | Updated: 2026-08-28 | 3 failing / 34 total
• Unbreak FPGA CI and correct two unbacked hardware claims #2081 Unbreak FPGA CI and correct two unbacked hardware claims | Created: 2026-08-11 | Updated: 2026-08-20 | 5 failing / 27 total

Summary

Status	Count
Total Open PRs	16
PRs with Failing Checks	13
PRs with All Checks Green	3
READY	2
FAILING	13
PENDING	0
NO CHECKS YET	0

These columns do not partition: 2 + 13 + 0 + 0 = 15, and there are 16 open PRs. A PR is being counted twice or not at all.

Seal Status

• ⚠️ STALE -- sha256(compiler.rs)=d4c5b22b471e != manifest seal=87e5cbd3ad94.
  The committed NMSE numbers were certified against an older compiler.rs.
  Run scripts/reseal-check.sh locally for the two-step reseal command (advisory; not a merge gate).