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docs: reorganise -- current reference gathered, finished work archived, superseded and dead ideas marked as such

Browse Source 
docs/CLAUDE.md Phase 2, 2026-10-14.  All moves by git mv; every archived
file carries a header saying what it is, why, and where to look instead.

- docs/reference/ (new): roadmap and versioning policy, M7.1, word-ACL
  design, kernel args, hosted acceptance test, dictionary, primitives,
  ontology, L8 table -- previously spread over docs/, docs/lithosananke/
  and docs/03-architecture/.
- docs/working/archive/historical/: finished work (session plan, test-gap
  audit, birthing plan, fix write-ups, the January architecture draft).
- docs/working/archive/superseded/: the Hermes-VM Tripod docs and July
  Hermes designs (-> FABRIC-3.5/3.6), the StarForth roadmap, every working
  doc already flagged superseded or obsolete.
- docs/working/archive/dead/: the hal_* target contract (never adopted),
  L4Re, metrics-and-knobs.
- Papers and proposals into docs/working/papers/.
- References rewritten across the repo (not logs/, not docs/patent/);
  CLAUDE.md's documentation section rewritten.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This commit is contained in:
rajames
2026-10-14 16:03:56 -04:00
co-authored by Claude Opus 5.5
parent 1a4b163861
commit 7aed588f78
116 changed files with 305 additions and 175 deletions
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docs/INDEX.md
+31 -31
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@@ -71,8 +71,8 @@
| docs/working/papers/ANTI_CLAIMS.md | Explicit boundary statements for SSRN/peer-review defensibility | CURRENT | Directly supports published SSRN paper; no code references that have drifted. |
| ./docs/CLAUDE.md | Docs-root instructions for Claude Code; two-tier doc model plan | WORKING | Describes a `docs/formal/` + `docs/working/` restructure not yet executed; active planning doc, not authoritative state ref (`.claude/CLAUDE.md` is). |
| docs/working/archive/COMPUTATIONAL_PHYSICS_FRAMEWORK.md | Expansive "physics of computation" claims framework | HISTORICAL | Contains strong over-claims ("This is not metaphor") that contradict `ANTI_CLAIMS.md` and `ACADEMIC_WORDING_GUIDELINES.md`; dates from earlier draft thinking (2025-12-10). |
| ./docs/DARPA_SSM_Proposal_James.docx | DARPA SSM grant proposal (Word format) | WORKING | Active proposal document; companion to the PDF version. |
| ./docs/DARPA_SSM_Proposal_James.pdf | DARPA SSM grant proposal (PDF) | WORKING | Active funding proposal; filename indicates a working/submission-ready draft. |
| ./docs/working/papers/proposals/DARPA_SSM_Proposal_James.docx | DARPA SSM grant proposal (Word format) | WORKING | Active proposal document; companion to the PDF version. |
| ./docs/working/papers/proposals/DARPA_SSM_Proposal_James.pdf | DARPA SSM grant proposal (PDF) | WORKING | Active funding proposal; filename indicates a working/submission-ready draft. |
| docs/working/archive/DOCUMENTATION_AUDIT.md | Docs audit from 2025-12-14; gap/inconsistency findings | HISTORICAL | Audit from a past triage pass; most findings have since changed; useful historical record. |
| docs/working/papers/EXECUTIVE_SUMMARY.md | Plain-English summary of StarForth results for non-specialists | CURRENT | Accurate, well-calibrated summary with correct metaphor framing; audience: journalists, admins, reviewers. |
| docs/working/papers/FINAL_REPORT/appendix_glossary.adoc | AsciiDoc glossary appendix for multi-chapter report | CURRENT | Formal, math-precise definitions consistent with current ontology; intended for book/report compilation. |
@@ -87,7 +87,7 @@
| docs/working/papers/REPRODUCIBILITY.md | One-command reproduction protocol with exact expected output | CURRENT | References valid build commands and `--doe` flag; expected output values consistent with published claims. |
| docs/working/papers/SCIENTIFIC_DEFENSE_CHECKLIST.md | Checklist of attack vectors and defenses for peer review | WORKING | Many "missing defenses" (GPG signing, Zenodo DOI, R/Python scripts) not yet addressed; still actively relevant. |
| docs/working/papers/SENSITIVITY_ANALYSIS.md | Parameter sweep design: robustness of 0% CV claim | CURRENT | Documents planned sensitivity experiments; scientifically sound framing; supports SSRN defensibility. |
| ./docs/SSM_DARPA_Complete_Proposal_James_FINAL.docx | DARPA SSM complete/final proposal (Word, FINAL) | WORKING | "FINAL" in name suggests submission-ready; likely supersedes `DARPA_SSM_Proposal_James.docx` but keep both until confirmed. |
| ./docs/working/papers/proposals/SSM_DARPA_Complete_Proposal_James_FINAL.docx | DARPA SSM complete/final proposal (Word, FINAL) | WORKING | "FINAL" in name suggests submission-ready; likely supersedes `DARPA_SSM_Proposal_James.docx` but keep both until confirmed. |
| docs/working/papers/SSRN_companion/Math_Companion_SSRN.pdf | Compiled PDF of math companion to SSRN paper | CURRENT | Rendered output of the `.tex` source; companion to the published SSRN paper. |
| docs/working/papers/SSRN_companion/Math_Companion_SSRN.tex | LaTeX source for math companion document | CURRENT | Source of record for comprehensive math/engineering structures reference; cross-references implementation. |
| docs/working/papers/SSRN_companion/figures/fig1_snake_trajectory.pdf | Figure asset: snake/phase trajectory | CURRENT | Figure asset for the SSRN math companion. |
@@ -97,31 +97,31 @@
| docs/working/papers/SSRN_companion/figures/fig5_bimodal_distributions.pdf | Figure asset: bimodal distributions | CURRENT | Figure asset for the SSRN math companion. |
| docs/working/papers/SSRN_companion/figures/fig6_performance_vs_k.pdf | Figure asset: performance vs K | CURRENT | Figure asset for the SSRN math companion. |
| docs/working/papers/SSRN_companion/figures/fig7_performance_by_regime.pdf | Figure asset: performance by regime | CURRENT | Figure asset for the SSRN math companion. |
| ./docs/SYSTEM_NARRATIVE.pdf | Compiled PDF of system narrative | CURRENT | Rendered output of `SYSTEM_NARRATIVE.tex`; technical story for patent counsel and reviewers. |
| ./docs/SYSTEM_NARRATIVE.tex | LaTeX source: technical narrative for patent/research review | CURRENT | Well-framed, correctly calibrated narrative; accurate description of the adaptive runtime and 90-run experiment. |
| ./docs/working/papers/SYSTEM_NARRATIVE.pdf | Compiled PDF of system narrative | CURRENT | Rendered output of `SYSTEM_NARRATIVE.tex`; technical story for patent counsel and reviewers. |
| ./docs/working/papers/SYSTEM_NARRATIVE.tex | LaTeX source: technical narrative for patent/research review | CURRENT | Well-framed, correctly calibrated narrative; accurate description of the adaptive runtime and 90-run experiment. |
| docs/working/scratch/TASK_LIST.md | AI/human task list with working rules and incremental tasks | WORKING | All tasks are unchecked; likely predates recent physics work; rules section is evergreen but specific tasks may be stale or partially done. |
| docs/working/archive/artifacts/kanban-workflow/MANIFEST.adoc | Artifact manifest for kanban workflow validation scripts | HISTORICAL | Tracks process-tooling artifacts from a past workflow setup session; no ongoing relevance to VM or kernel. |
| docs/working/scratch/assets/README.md | Binary assets holding area README | WORKING | Correctly flags `book-FIXED.docx` etc. as misplaced; the guidance (move to LFS/external) is still actionable. |
| docs/working/scratch/assets/book-FIXED.docx | Book/report Word document | WORKING | Binary asset misplaced in docs/assets; should move to LFS per assets/README.md guidance. |
| docs/working/architecture/heartbeat_csv_export.md | Heartbeat CSV export design: format, columns, TODO status | WORKING | Several columns marked `⚠️ TODO`; matches CLAUDE.md note that `heartbeat_export_csv()` is not yet implemented; active design/tracking doc. |
| ./docs/ontology.pdf | Compiled PDF of `ontology.tex` | CURRENT | Rendered output of `ontology.tex`; self-contained reference for academic inclusion. |
| ./docs/ontology.tex | LaTeX source for formal ontology | CURRENT | Source of record matching `ONTOLOGY.md` content; used for journal/conference paper inclusion. |
| ./docs/working/papers/ontology.pdf | Compiled PDF of `ontology.tex` | CURRENT | Rendered output of `ontology.tex`; self-contained reference for academic inclusion. |
| ./docs/working/papers/ontology.tex | LaTeX source for formal ontology | CURRENT | Source of record matching `ONTOLOGY.md` content; used for journal/conference paper inclusion. |
| docs/working/archive/prog-prove.pdf | Unknown — likely Isabelle/HOL or proof-assistant tutorial PDF | HISTORICAL | Filename suggests a proof-programming reference; not authored by this project; reference material only. |
| docs/working/architecture/getting-started/DEVELOPER.md | Dev environment setup, Isabelle install | CURRENT | Generic setup instructions still match current build system. |
| docs/working/architecture/getting-started/README.md | Getting-started index/TOC | CURRENT | Navigation page; links resolve to existing files. |
| docs/working/architecture/getting-started/quick-start/factorial-doe.md | Quick-start for 2^6 per-loop factorial DoE | OBSOLETE | Describes retired `ENABLE_LOOP_1..6` compile-time toggles; replaced by L8 Jacquard runtime mode selector. Hardcoded `/home/rajames/...` paths. |
| docs/working/archive/superseded/factorial-doe/quick-start.md | Quick-start for 2^6 per-loop factorial DoE | OBSOLETE | Describes retired `ENABLE_LOOP_1..6` compile-time toggles; replaced by L8 Jacquard runtime mode selector. Hardcoded `/home/rajames/...` paths. |
| docs/working/architecture/getting-started/quick-start/heartbeat-doe.md | Quick-start for heartbeat DoE run | HISTORICAL | Dated 2025-11-20, references a specific completed run directory and hardcoded user paths. |
| docs/working/architecture/getting-started/quick-start/optimization-doe.md | Quick-start for 5-opportunity optimization DoE | HISTORICAL | References dated result dirs from a completed tuning campaign; superseded conceptually by L8's data-driven design. |
| docs/working/experiments/02-experiments/L8_WIRING_CODE_REVIEW_GUIDE.md | Code review guide for L8 wiring (L2/L3/L5/L6) | HISTORICAL | Dated 2025-12-05; matches current `physics_metadata.c` — completed, accurate review record. |
| docs/working/experiments/02-experiments/L8_WIRING_IMPLEMENTATION_SUMMARY.md | Summary of L8 gating implementation | HISTORICAL | Dated 2025-12-05, marked complete; verified consistent with current source. |
| docs/working/experiments/02-experiments/L8_WIRING_PLAN.md | Plan for wiring loops to L8 mode selector | SUPERSEDED | Superseded by L8_WIRING_IMPLEMENTATION_SUMMARY.md and L8_WIRING_CODE_REVIEW_GUIDE.md (plan was executed and reviewed). |
| docs/working/archive/superseded/L8_WIRING_PLAN.md | Plan for wiring loops to L8 mode selector | SUPERSEDED | Superseded by L8_WIRING_IMPLEMENTATION_SUMMARY.md and L8_WIRING_CODE_REVIEW_GUIDE.md (plan was executed and reviewed). |
| docs/working/experiments/02-experiments/README.md | Experiments directory index | CURRENT | Accurately lists existing subdirectories. |
| docs/working/experiments/02-experiments/factorial-doe/guide.md | Full 2^6 factorial DoE guide | OBSOLETE | Describes retired per-loop Makefile-toggle architecture, replaced by L8 Jacquard. |
| docs/working/experiments/02-experiments/factorial-doe/incompatible-configs.md | Handling incompatible factorial loop configs | OBSOLETE | Build-time incompatibility handling for the retired 2^6 toggle experiment. |
| docs/working/experiments/02-experiments/factorial-doe/index.md | Index for factorial DoE docs | OBSOLETE | Points to stale doc paths; describes retired architecture. |
| docs/working/experiments/02-experiments/factorial-doe/workflow.md | Factorial DoE data pipeline workflow | HISTORICAL | Documents completed 2025-11-19 factorial campaign that produced data behind current L8 design; toggle architecture retired. |
| docs/working/experiments/02-experiments/heartbeat-doe/corrected-design.md | Heartbeat DoE corrected metric design | SUPERSEDED | Superseded by phase2-corrected.md ("corrected and finalized" version). |
| docs/working/experiments/02-experiments/heartbeat-doe/design.md | Original Phase 2 heartbeat DoE design | SUPERSEDED | Pre-correction draft; superseded by corrected-design.md / phase2-corrected.md. |
| docs/working/archive/superseded/factorial-doe/guide.md | Full 2^6 factorial DoE guide | OBSOLETE | Describes retired per-loop Makefile-toggle architecture, replaced by L8 Jacquard. |
| docs/working/archive/superseded/factorial-doe/incompatible-configs.md | Handling incompatible factorial loop configs | OBSOLETE | Build-time incompatibility handling for the retired 2^6 toggle experiment. |
| docs/working/archive/superseded/factorial-doe/index.md | Index for factorial DoE docs | OBSOLETE | Points to stale doc paths; describes retired architecture. |
| docs/working/archive/superseded/factorial-doe/workflow.md | Factorial DoE data pipeline workflow | HISTORICAL | Documents completed 2025-11-19 factorial campaign that produced data behind current L8 design; toggle architecture retired. |
| docs/working/archive/superseded/heartbeat-doe-corrected-design.md | Heartbeat DoE corrected metric design | SUPERSEDED | Superseded by phase2-corrected.md ("corrected and finalized" version). |
| docs/working/archive/superseded/heartbeat-doe-design.md | Original Phase 2 heartbeat DoE design | SUPERSEDED | Pre-correction draft; superseded by corrected-design.md / phase2-corrected.md. |
| docs/working/experiments/02-experiments/heartbeat-doe/execution-guide.md | How to run Phase 2 heartbeat DoE | HISTORICAL | Dated 2025-11-20, hardcoded stale path; describes running the now-superseded design. |
| docs/working/experiments/02-experiments/heartbeat-doe/implementation-summary.md | Deliverables summary for heartbeat DoE | HISTORICAL | Point-in-time "complete" status snapshot dated 2025-11-20 for pre-correction design. |
| docs/working/experiments/02-experiments/heartbeat-doe/phase2-corrected.md | Final corrected heartbeat DoE design | WORKING | Latest version in the revision chain; still describes not-yet-fully-implemented work. |
@@ -134,27 +134,27 @@
| docs/working/architecture/03-architecture/OVERVIEW.md | Top-level architecture overview (3-layer model, physics loops, boot sequence) | WORKING | Header says "Status: Complete, 2025-12-14" but roadmap still frames StarKernel as "PLANNED"/HAL migration "IN PROGRESS," lagging CLAUDE.md's actual M0-M6-done/M7-in-progress state; needs a refresh pass. |
| docs/working/architecture/03-architecture/README.md | Directory index/landing page for 03-architecture/ | WORKING | Shorter duplicate of OVERVIEW.md's roadmap; same staleness (treats StarKernel as not-yet-started); functions as nav index, content needs sync with CLAUDE.md. |
| docs/working/architecture/03-architecture/adaptive-systems/adaptive-window-and-decay.md | Root-cause investigation: rolling-window shrink + decay_slope placeholder bugs | HISTORICAL | Dated 2025-11-08, "Root Cause Analysis Complete." Diagnostic/incident report; trigger doc for window-inference-redesign.md. |
| docs/working/architecture/03-architecture/adaptive-systems/loop-5-sketch.md | Alternate Loop #5 proposal: prefetch-accuracy-driven binary-chop window tuning | SUPERSEDED | Superseded by window-inference-redesign.md. Undated draft ending in an open question to the user (never approved); the shipped Loop #5 uses Levene's test, not this mechanism. |
| docs/working/archive/superseded/loop-5-sketch.md | Alternate Loop #5 proposal: prefetch-accuracy-driven binary-chop window tuning | SUPERSEDED | Superseded by window-inference-redesign.md. Undated draft ending in an open question to the user (never approved); the shipped Loop #5 uses Levene's test, not this mechanism. |
| docs/working/architecture/03-architecture/adaptive-systems/multivariate-dynamics.md | Phase 2 DoE experiment design: multivariate stability fingerprinting across 7 metrics | WORKING | Dated 2025-11-20, "Status: Design Phase." Forward-looking proposal tied to still-unimplemented heartbeat instrumentation. |
| docs/working/architecture/03-architecture/adaptive-systems/window-inference-redesign.md | Redesign of window-width inference using Levene's test on disjoint chunks | CURRENT | Dated 2025-11-19, "DESIGN (approved for implementation)." Matches the Loop #5/#6 mechanism CLAUDE.md/OVERVIEW.md describe as actually implemented (inference_engine.c). |
| docs/working/architecture/03-architecture/hal/README.md | Index/reading-order guide for HAL doc set | WORKING | Status table claims all 5 HAL docs "Complete, 2025-12-14," but describes target architecture per overview.md's own disclaimer, not built code; misleading without that caveat. |
| docs/working/architecture/03-architecture/hal/interfaces.md | hal_* C interface contract spec (time, interrupt, memory, console, cpu, panic) | WORKING | Normative target API design; current codebase uses sf_time_backend_t-style naming per overview.md — this HAL layer is not yet built as specified. |
| docs/working/architecture/03-architecture/hal/migration-plan.md | 7-phase plan to migrate codebase to hal_* interfaces | WORKING | Forward plan ("Phase 2 IN PROGRESS" per roadmap); CLAUDE.md's current source tree shows this migration not yet executed. |
| docs/working/architecture/03-architecture/hal/overview.md | HAL rationale/design-principles doc | WORKING | Contains the key disclaimer: "current codebase uses sf_time_backend_t... different naming" — explicitly flags the whole HAL doc family as target/aspirational, not current. |
| docs/working/architecture/03-architecture/hal/platform-implementations.md | Example hal_* implementations for Linux and kernel platforms | OBSOLETE | Assumes src/platform/<platform>/hal_*.c layout; actual built StarKernel tree (per CLAUDE.md) uses src/starkernel/{arch,boot,capsule,hal,memory,...} — a different, already-implemented structure. |
| docs/working/architecture/03-architecture/hal/starkernel-integration.md | Kernel HAL integration guide, src/platform/kernel/ layout, milestone roadmap to "ok" prompt | OBSOLETE | Describes Milestone 1 "Boot + Serial Output" as a starting point; LithosAnanke is actually at v1.0.8 with M0-M6 complete, M7 in progress, using a wholly different src/starkernel/ directory structure. |
| docs/working/archive/dead/hal-target-contract/README.md | Index/reading-order guide for HAL doc set | WORKING | Status table claims all 5 HAL docs "Complete, 2025-12-14," but describes target architecture per overview.md's own disclaimer, not built code; misleading without that caveat. |
| docs/working/archive/dead/hal-target-contract/interfaces.md | hal_* C interface contract spec (time, interrupt, memory, console, cpu, panic) | WORKING | Normative target API design; current codebase uses sf_time_backend_t-style naming per overview.md — this HAL layer is not yet built as specified. |
| docs/working/archive/dead/hal-target-contract/migration-plan.md | 7-phase plan to migrate codebase to hal_* interfaces | WORKING | Forward plan ("Phase 2 IN PROGRESS" per roadmap); CLAUDE.md's current source tree shows this migration not yet executed. |
| docs/working/archive/dead/hal-target-contract/overview.md | HAL rationale/design-principles doc | WORKING | Contains the key disclaimer: "current codebase uses sf_time_backend_t... different naming" — explicitly flags the whole HAL doc family as target/aspirational, not current. |
| docs/working/archive/dead/hal-target-contract/platform-implementations.md | Example hal_* implementations for Linux and kernel platforms | OBSOLETE | Assumes src/platform/<platform>/hal_*.c layout; actual built StarKernel tree (per CLAUDE.md) uses src/starkernel/{arch,boot,capsule,hal,memory,...} — a different, already-implemented structure. |
| docs/working/archive/dead/hal-target-contract/starkernel-integration.md | Kernel HAL integration guide, src/platform/kernel/ layout, milestone roadmap to "ok" prompt | OBSOLETE | Describes Milestone 1 "Boot + Serial Output" as a starting point; LithosAnanke is actually at v1.0.8 with M0-M6 complete, M7 in progress, using a wholly different src/starkernel/ directory structure. |
| docs/working/architecture/03-architecture/heartbeat-system/architecture.md | Proposes vm_tick() dispatcher centralizing Loop #3/#5 heartbeat logic | HISTORICAL | No date; ends in an open question, never confirmed adopted. Foundational rationale doc; superseded in specifics by instrumentation-plan.md's HeartbeatTickSnapshot design. |
| docs/working/architecture/03-architecture/heartbeat-system/critical-insight.md | Discovery memo: heartbeat tick rate is variable, not fixed; Stage 1 DoE baseline was flawed | HISTORICAL | Dated 2025-11-20, "Game-changer for Phase 2 DoE." Point-in-time investigation memo that directly motivated implementation-plan.md. |
| docs/working/architecture/03-architecture/heartbeat-system/implementation-plan.md | Plan for HeartbeatRateSample logging to capture variable tick rate | SUPERSEDED | Superseded by instrumentation-plan.md. Same date (2025-11-20) and goal, but proposes an earlier/different struct (HeartbeatRateSample) than the HeartbeatTickSnapshot design CLAUDE.md cites as the live target. |
| docs/working/archive/superseded/heartbeat-rate-logging-plan.md | Plan for HeartbeatRateSample logging to capture variable tick rate | SUPERSEDED | Superseded by instrumentation-plan.md. Same date (2025-11-20) and goal, but proposes an earlier/different struct (HeartbeatRateSample) than the HeartbeatTickSnapshot design CLAUDE.md cites as the live target. |
| docs/working/architecture/03-architecture/heartbeat-system/instrumentation-plan.md | Per-tick instrumentation plan: HeartbeatTickSnapshot, tick_buffer, heartbeat_export_csv() | WORKING | Explicitly the doc CLAUDE.md cites as current ("declared in include/vm.h, but heartbeat_export_csv() is not yet implemented"). Checklist entirely unchecked. |
| docs/working/architecture/03-architecture/heartbeat-system/segfault-analysis.md | Root-cause analysis of heartbeat-thread/main-thread race on RollingWindowOfTruth | HISTORICAL | Dated 2025-11-19, "Identified & Ready for Fix," includes a past-tense commit-message template implying the tuning_lock fix was applied. No current doc mentions this race as open. |
| docs/working/architecture/03-architecture/physics-engine/feedback-loops-analysis.md | Investigative bug-hunt audit of 6 feedback loops (precursor to the 7-loop model) | SUPERSEDED | Superseded by feedback-loops.md. Dated 2025-11-08, full of strikethrough "FIXED" headers; covers only 6 loops, unlike the polished current 7-loop reference. |
| docs/working/archive/superseded/feedback-loops-analysis.md | Investigative bug-hunt audit of 6 feedback loops (precursor to the 7-loop model) | SUPERSEDED | Superseded by feedback-loops.md. Dated 2025-11-08, full of strikethrough "FIXED" headers; covers only 6 loops, unlike the polished current 7-loop reference. |
| docs/working/architecture/03-architecture/physics-engine/feedback-loops.md | Canonical reference: all 7 feedback loops, tuning knobs, related source files | CURRENT | Matches CLAUDE.md's explicit citation ("all 7 loops detailed") verbatim; clean finished reference table covering Loops #1-7 including #5/#6 inference. |
| docs/working/architecture/03-architecture/physics-engine/metrics-and-knobs.md | Gap-analysis backlog of metrics not yet collected (stack depth, bucket histograms, etc.) | WORKING | Explicitly self-titled "GAPS ONLY"; prioritized TODO backlog, not a current-state description; some gaps may have since been filled. |
| docs/working/archive/dead/metrics-and-knobs.md | Gap-analysis backlog of metrics not yet collected (stack depth, bucket histograms, etc.) | WORKING | Explicitly self-titled "GAPS ONLY"; prioritized TODO backlog, not a current-state description; some gaps may have since been filled. |
| docs/working/architecture/03-architecture/physics-engine/monitoring-principles.md | Doctrinal rules for non-perturbative monitoring instrumentation | CURRENT | Presents itself as binding/evergreen ("canonical rules for ALL AI assistants"); uses an older "four core loops (FL1-FL4)" framing that should be reconciled with the current 7-loop model, but the doctrine itself remains in force. |
| docs/working/architecture/03-architecture/physics-engine/ssm-equations.md | Exploratory mathematical modeling of SSM via physics analogies for patent/DARPA strategy | HISTORICAL | Dated 2025-11-29, self-labeled "Status: Research Analysis - Exploratory." Predates Jacquard naming; speculates generically about future "L8" without Jacquard/attractor-bucket/mode-name vocabulary. |
| docs/working/architecture/03-architecture/physics-engine/ssm-raw-data-analysis.md | Raw experimental data analysis from a specific Nov 22-27 2025 DoE campaign (51,840 runs) | HISTORICAL | Dated 2025-11-29; tied to specific named CSV files and a calendar-based "Next Steps" plan. Uses "L8" and 4 of 6 Jacquard mode names but never "Jacquard" — an early/transitional naming stage. |
| docs/working/architecture/03-architecture/physics-engine/steady-state-machine.md | Formal theoretical definition of SSM as a computational model (attractor basins, axioms) | OBSOLETE | Zero mentions of "Jacquard," "L8," "attractor bucket," or the six named modes from CLAUDE.md; reads as a conceptual precursor never reconciled with the concrete ssm_jacquard.c system. |
| docs/working/archive/superseded/steady-state-machine.md | Formal theoretical definition of SSM as a computational model (attractor basins, axioms) | OBSOLETE | Zero mentions of "Jacquard," "L8," "attractor bucket," or the six named modes from CLAUDE.md; reads as a conceptual precursor never reconciled with the concrete ssm_jacquard.c system. |
| docs/working/architecture/03-architecture/pipelining/context-window-and-binary-chop.md | Context-window infrastructure (Knob #6) + planned binary-chop tuning for Loop #4 | WORKING | Dated 2025-11-06, "Phase 1 Extension Complete," but binary-chop decision logic explicitly a doubling-rule stub with "Phase 2 (Next session)" unchecked; corroborated as still-unutilized by wired-not-utilized.md. |
| docs/working/architecture/03-architecture/pipelining/design.md | Master architectural design for pipelining/speculative execution (Loop #4) | HISTORICAL | No date/status stamp; entirely aspirational ("Goal:", "Hypothesis"); Phase 3+ (actual prefetching/speculation) roadmap items remain unchecked and appear unrealized per wired-not-utilized.md. |
| docs/working/architecture/03-architecture/pipelining/phase-1-instrumentation.md | Completed-checkpoint record of Phase 1 transition-tracking instrumentation | HISTORICAL | Dated 2025-11-06, "Phase 1 Complete," 731 tests passing — accurate closed record of one sub-phase; its Phase 2-4 TODOs were never closed per wired-not-utilized.md. |
@@ -229,7 +229,7 @@
| ./docs/patent/final_provisional/sb0016.pdf | USPTO form SB0016 — filed copy | CURRENT | Differs from root `sb0016.pdf` (577171 vs 557654 bytes); this larger copy is the filed/submitted version and is the more complete document. |
| ./docs/patent/final_provisional/ssm_RAJ_v1_patent_application.pdf | Compiled patent application PDF — filed copy | SUPERSEDED | Byte-identical to root `ssm_RAJ_v1_patent_application.pdf` (1735085 bytes); root copy is the working canonical version. |
| docs/working/scratch/src/INTEGRATION_NOTES.adoc | StarForth↔StarshipOS sync scripts (integrator.sh) | HISTORICAL | Describes ad-hoc integrator.sh scripts and one-day debugging session; superseded by formal capsule/build pipeline in current CLAUDE.md. Worth keeping as record of integration approach. |
| docs/working/scratch/src/L4RE_INTEGRATION_TODO.adoc | L4Re integration checklist, hardcoded local paths | OBSOLETE | References absolute local dev paths (`/home/rajames/CLionProjects/...`) and a TODO checklist for copying platform files; current architecture has moved on. |
| docs/working/archive/dead/l4re/L4RE_INTEGRATION_TODO.adoc | L4Re integration checklist, hardcoded local paths | OBSOLETE | References absolute local dev paths (`/home/rajames/CLionProjects/...`) and a TODO checklist for copying platform files; current architecture has moved on. |
| docs/working/scratch/src-index.adoc | docs/src documentation index | WORKING | Active index/TOC for the docs/src tree, but contains multiple dead links (ABI.adoc, BLOCK_STORAGE_GUIDE.adoc, WORD_DEVELOPMENT.adoc, TESTING.adoc, BREAK_ME_REPORT.adoc, GAP_ANALYSIS.adoc) — needs pruning/repair. |
| docs/working/architecture/architecture-internals/INIT_SYSTEM.adoc | INIT system / conf/init.4th boot mechanism | CURRENT | Describes init.4th, INIT word, dictionary fence — matches current capsule/init architecture described in CLAUDE.md. |
| docs/working/architecture/architecture-internals/MESSAGING.adoc | Thermodynamic "Message Field" model for StarshipOS IPC | WORKING | Forward-looking design doc for a not-yet-implemented StarshipOS messaging subsystem; consistent with physics/thermodynamic metaphor language. |
@@ -270,11 +270,11 @@
| docs/working/hardware/performance-profiling/ARM64_OPTIMIZATIONS.adoc | ARM64 assembly optimization summary | CURRENT | Referenced headers (`include/vm_asm_opt_arm64.h`, `vm_inner_interp_arm64.h`, `arch_detect.h`) all confirmed present in current `include/` tree. |
| docs/working/hardware/performance-profiling/ASM_OPTIMIZATIONS.adoc | x86_64 assembly optimization guide | CURRENT | Referenced headers (`vm_asm_opt.h`, `vm_inner_interp_asm.h`) confirmed present; consistent with `USE_ASM_OPT=1` build flag in current CLAUDE.md. |
| docs/working/hardware/performance-profiling/PROFILER.adoc | Built-in word-execution profiler guide | CURRENT | Describes profiler integrated with PGO pipeline; consistent with `make test PROFILE=1` and `profiler.c` present in current src tree. |
| docs/working/hardware/platform-integration/L4RE_DICTIONARY_ALLOCATION.adoc | Dictionary allocation strategy proposal for L4Re | WORKING | References `src/dictionary_management.c:228` (`vm_create_word()` malloc) and `defining_words.c:554` (`FORGET` free) — both locations exist; malloc/free dependency has likely not yet been replaced with L4Re-native allocator. |
| docs/working/hardware/platform-integration/L4RE_INTEGRATION.adoc | General L4Re integration guide (IPC, dataspaces, package structure) | WORKING | Broad integration guide; L4Re remains a supported platform per CLAUDE.md tech stack diagram. |
| docs/working/archive/dead/l4re/L4RE_DICTIONARY_ALLOCATION.adoc | Dictionary allocation strategy proposal for L4Re | WORKING | References `src/dictionary_management.c:228` (`vm_create_word()` malloc) and `defining_words.c:554` (`FORGET` free) — both locations exist; malloc/free dependency has likely not yet been replaced with L4Re-native allocator. |
| docs/working/archive/dead/l4re/L4RE_INTEGRATION.adoc | General L4Re integration guide (IPC, dataspaces, package structure) | WORKING | Broad integration guide; L4Re remains a supported platform per CLAUDE.md tech stack diagram. |
| docs/working/hardware/platform-integration/PLATFORM_ABSTRACTION.adoc | Platform abstraction layer (vtable pattern for POSIX/L4Re) | CURRENT | Matches actual `platform/linux/time.c` and `platform/l4re/time.c` files present in current src tree per CLAUDE.md source tree listing. |
| docs/working/hardware/platform-integration/RASPBERRY_PI_BUILD.adoc | Raspberry Pi 4 / ARM64 build guide | CURRENT | Matches `rpi4-cross` Makefile target and ARM64 architecture support (`ARCH=raspi`) listed in current CLAUDE.md build targets. |
| docs/working/hardware/platform-integration/l_4_re_blkio_endpoints.adoc | Block I/O L4Re porting endpoints (blkio vtable mapping) | CURRENT | Describes `blkio_open/close/read` vtable API; matches `blkio_*.c` backend files listed in current CLAUDE.md source tree. |
| docs/working/archive/dead/l4re/l_4_re_blkio_endpoints.adoc | Block I/O L4Re porting endpoints (blkio vtable mapping) | CURRENT | Describes `blkio_open/close/read` vtable API; matches `blkio_*.c` backend files listed in current CLAUDE.md source tree. |
| docs/working/scratch/testing-quality/KANBAN-WORKFLOW-VALIDATION.adoc | Validation procedure for GitHub Projects Kanban automation (CAPA-032) | CURRENT | Dated 2025-11-02 with explicit source commit hash; references `.github/workflows/capa-kanban-sync.yml` which is a concrete CI artifact. |
| docs/working/archive/legacy/OPTIMIZATION_OPPORTUNITIES.md | Physics engine optimization opportunity ranking dated 2025-11-19 | SUPERSEDED | Superseded by docs/03-architecture/physics-engine/ and Loop #5/#6 implementations |
| docs/working/archive/legacy/README.md | Index and usage guide for the docs/archive directory | CURRENT | Self-referential; accurately describes the archive's purpose and sub-structure |
@@ -290,7 +290,7 @@
| docs/working/archive/legacy/phase-1/Reference/PHASE_1_TESTING_RESULTS.md | Phase 1 testing results summary | HISTORICAL | Test results from Phase 1 CI/governance work |
| docs/working/archive/legacy/phase-1/Reference/PHYSICS_EXPERIMENT_README.md | README for the 90-run physics validation experiment | HISTORICAL | Companion README to the experiment data in physics_experiment/ |
| docs/working/archive/legacy/phase-1/Reference/RULE_1_GATES_IMPLEMENTATION.md | Implementation notes for Rule 1 CI gating | HISTORICAL | CI gate design decisions from Phase 1 |
| docs/working/archive/legacy/phase-1/Reference/SECURITY.md | Security notes predating the ACL system | HISTORICAL | Pre-ACL security model; superseded by docs/03-architecture/word-acl/DESIGN.md |
| docs/working/archive/legacy/phase-1/Reference/SECURITY.md | Security notes predating the ACL system | HISTORICAL | Pre-ACL security model; superseded by docs/reference/word-acl/DESIGN.md |
| docs/working/archive/legacy/phase-1/Reference/SESSION_SUMMARY.md | Transient AI session summary | HISTORICAL | Session-level notes; limited long-term value |
| docs/working/archive/legacy/phase-1/Reference/TEST-CAPA-TEMPLATE.md | CAPA test case template | HISTORICAL | Template used during Phase 1 CAPA process |
| docs/working/archive/legacy/phase-1/Reference/codex_audit_report.md | Codex audit report of the codebase | HISTORICAL | Point-in-time static analysis or review; may be stale |