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Manuscript and supplementary content map

Historical intake index, October 12, 2026. Companion source/protocol/context URLs now route to consolidated canonical pages; use the reviewer guide.

The short JOSS draft carries the software contribution. The longer manuscript and SI carry design history, contracts, source distinctions, protocol details, and dated evidence. This map gives every numbered section, table, and figure a documentation home while retaining the complete originals and references. It records the intake on October 12, 2026; the PDFs themselves use a September 25, 2026 evidence boundary.

The six linked companion pages below adapt the longer material into readable website documentation. Existing generated references retain ownership of live signatures and catalog facts. Historical results are attributed to their recorded revisions, not relabeled as fresh validation.

Main manuscript

Source section	Documentation home
Abstract; §1 introduction; §1.1 definitions and scope	Scientific inspectability, glossary, local trace scope
§2 narrative pipelines and shared grammar	Design origins and related systems
§3 layered design; §3.1 source-qualified nouns	Local trace and evidence layers, source comparison, noun library
§3.2 verbs, order, state and trace	Condition contracts, local traces, temporal alignment
§3.3 ordinary objects and project extensions	Local trace and callable boundaries, custom verbs
§3.4 evidence beneath abstraction	Source evidence layers
§4 worked protocol	Working Lands protocol, executable vignette
§5 verification and semantic consistency	Evidence and triage, validation methods
§6.1 evidence limits	Archival requirements and claim boundaries
§6.2 community of vocabularies	Contribution routes, core and projects
§6.3 larger synthesis and agent hypothesis	Future synthesis, limitations
§7 conclusion	Scientific inspectability and the scope of the companion pages
§8 data, code and release status	Software states and submission archive
AI statement; contributions; competing interests; acknowledgements	Retained verbatim in main p. 13; JOSS statements remain author-review material
References	Complete in main pp. 13–22; scholarly context in related systems

Supplementary information

Source section and subsections	Documentation home
S1 version boundaries	Evidence and software states
S2 origin, users, contribution	Design origins and contribution routes
S3 related numerical, workflow, domain systems	Related systems
S4 architecture; S4.1 glossary	Local trace layers, scientific inspectability, glossary
S5.1 state; S5.2 trace; S5.3 branch/callable boundaries	Local traces and workflow provenance, semantic grammar
S6.1 order; S6.2 conditional equivalence; S6.3 events	Condition and order contracts, events/episodes
S7 rule status; S7.1 condition; S7.2 missingness; S7.3 contract matrix; S7.4 units	Condition contracts and missing observations, generated verbs
S8.1 alignment; S8.2 support	Temporal alignment, source comparison
S8.3 ordinary objects; S8.4 plotting	Local object boundaries, condition rendering, visualization API
S9.1 catalog; S9.2 candidates	Source comparison, library, candidate readiness
S10.1 layers; S10.2 Phase 1; S10.3 live status	Source evidence, Phase 1 QA
S11 vignette inventory	Teaching roles and source evidence, current vignettes
S12.1 input; S12.2 statement; S12.3 acceptance	Working Lands protocol, decision validation
S13.1 execution/rejection; S13.2 classification; S13.3 revision-specific evidence	Verification and triage, RC1 report
S14 secondary extensions and namespace	Evidence boundaries, callable inventory
S15 reproduction and repository evidence map	Reproduction routes, validation
S16 rc3 and first-use fixes	First-use evidence, runtime identity
S17 claim-to-evidence matrix	Claim boundaries
S18 limitations and archive; agent hypothesis	Archival requirements, future synthesis
References	Complete in SI pp. 27–35; the shorter JOSS BibTeX does not replace this bibliography

Tables figures and equation

Source object	Home and retained original
Main Figure 1, order semantics	Order contracts; supplied figure extracted for JOSS; original p. 2
Main Figure 2, inspection layers	Local traces; original p. 6
Main Table 1, technical traditions	Related systems; original p. 5
Main Table 2, protocol boundaries	Working Lands; original p. 9
Main Table 3, claims	Evidence; original p. 10
SI Figure S1, layered grammar	Local trace layers; original p. 5
SI Figure S2, triage	Evidence and triage; original p. 22
SI equation 1, conditional equivalence	Condition and order contracts; original p. 10
SI Table S1	Software states; original p. 3
SI Table S2	Contribution routes; original p. 4
SI Table S3	State vocabulary; original p. 8
SI Tables S4–S8	Order, rule status, condition and verb contracts and current verb reference; original pp. 9–12
SI Table S9	Rendering contract; original p. 14
SI Tables S10–S15	Source comparison, candidates, QA and teaching roles; original pp. 15–18
SI Tables S16–S17	Working Lands input and branch records, local traces; original pp. 18–19
SI Tables S18–S21	Behavior, finding classification and revision evidence; original pp. 20–22
SI Table S22	Extension status; original p. 23
SI Table S23	Reproduction/evidence routes and existing pages linked throughout this map; original p. 24
SI Tables S24–S25	Claim-to-evidence matrix; original pp. 25–26

Editorial items remain editorial

The supplied JOSS draft includes pre-submission instructions about release wording, archival gaps, funding, and AI disclosure. They are preserved for collaborators to review, rather than treated as instructions to publish, modify release metadata, change scientific assumptions, or remove exports. The manuscript's author responsibility and funding statements need human confirmation. The PDF disclosure and JOSS disclosure differ in their account of completed human review; retaining both does not resolve that discrepancy.

This is a content migration with complete source preservation, not a new scientific evaluation or certification. Exact signatures remain generated; historical evidence remains dated; outstanding archival work remains visible.