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Chris Sweet edited this page Jun 12, 2026 · 38 revisions

type: index up: "Home_llm-wiki-memory-template"

Log — llm-wiki-memory-template

Chronological record of wiki activity.

[2026-05-20] create | Wiki initialized

  • by: Chris Sweet via claude-code
  • Scaffolded wiki structure with namespaced navigation files (Home, index, log, SCHEMA) authored to match the canonical create-mode output of wiki/init-wiki.sh
  • Wiki cloned to sibling path ../llm-wiki-memory-template.wiki/ rather than wiki/<repo>.wiki/ to avoid semantic collision with the template's wiki/ scaffolding directory; consequence: Home_<repo> up: "[[WIKI-INDEX]]" is a deliberate dangling reference for this layout
  • Ready for first ingest

[2026-05-20] ingest | Initial knowledge dump of template pattern, mechanisms, lessons, limitations

  • by: Chris Sweet via claude-code
  • Authored 18 content pages across five categories: foundation (5: Wiki-LLM-Pattern, Three-Operations, Template-vs-Derived-Projects, Agent-Overlays, Typed-Edges-and-Frontmatter), mechanisms (6: Knowledge-Graph-Pipeline, Verification-Gate, Discipline-Gates, PostToolUse-Hook, Log-Entry-Attribution, Sync-Flow), lessons (3: Parallel-File-Drift, Hook-Type-Matters, Validation-Methodology), limitations (3: Prompt-Injection-Residual, Inverse-Edges-Missing, Untested-Overlays), and applied examples (1: Microelectronics-Tutor-Demo)
  • Captured the substance of merged PRs: PR #1 (discipline gates, verification gate, PostToolUse hook) and PR #4 (log entry attribution, one-commit-per-entry), including the review feedback patterns and post-mortem lessons surfaced during structural + behavioral testing
  • Filed three open limitations explicitly: prompt-injection residual risk (not pattern-specific), missing edge inverses (issue #3, surfaced during PR #4 behavioral testing), and untested non-Claude-Code overlays (Cursor, none)
  • Used typed edges (extends:, criticizes:, supports:) wherever the relationship is clear; treated criticizes: as the right edge from a Limitation page to the concept it limits, and from a Lesson page to the prior approach it corrects
  • Index updated with all 18 pages organized by category; every page has at least 2 outbound links and a See also section
  • Verification gate criteria all pass: index updated, log entry being appended (this one), cross-references bidirectional, frontmatter present and non-untyped on every page

[2026-05-23] ingest | Governance — three-tier model for proliferating variants

  • by: Chris Sweet via claude-code
  • Filed Governance in the Foundation category in response to the wiki-llm pattern spreading beyond the base template into specialized variants (chrissweet/llm-wiki-tutor-template, with codebase-onboarding and grant-authoring siblings under discussion after the symposium demo and SIMBA collaboration)
  • The page extends Template-vs-Derived-Projects by introducing a third tier (variant template) between the base and an instantiated project; the placement rule, fork-vs-flag criteria, rebase discipline, graduation trigger, and ownership / drift detection all derive from the three-tier model
  • Cross-references the existing Sync-Flow for the ALWAYS_FILES contract (escalated one tier — variants rebase from base the same way derived projects rebase from variants) and Lesson-Parallel-File-Drift for the same footgun escalated to the variant tier
  • Three open questions flagged for resolution as the variant population grows beyond two or three: variant discovery, versioning (pin to SHA vs HEAD), cross-variant features
  • Home and Index updated in the Foundation category adjacent to Template-vs-Derived-Projects

[2026-05-31] lint | Reconcile wiki with template code; flag KG aspirational; fix none-overlay framing

  • by: Chris Sweet via claude-code
  • Audited the wiki against crcresearch/llm-wiki-memory-template main after reading all 24 pages. Triggered by an MVP-planning exercise that needed accurate references to template wiki pages.
  • Three substantive drifts found, all corrected in commit 8601db0:
    • Knowledge-Graph-Pipeline was described as implemented across 8 pages; reality is scripts/kg/build-graph.sh does not exist on main. Flagged status: aspirational with a "NOT YET IMPLEMENTED" banner; the design content preserved. Citations on the 7 dependent pages (Home, index, SCHEMA, Wiki-LLM-Pattern, Three-Operations, Typed-Edges-and-Frontmatter, Limitation-Inverse-Edges-Missing) softened to "designed, not yet implemented".
    • Limitation-Untested-Overlays and Agent-Overlays misframed --agent=none (a no-install flag in instantiate.sh) as a wiki/agents/none/ overlay. Reframed; minimal mode now described accurately as no-install. Also fixed: the claim that the README uses the phrase "untested-live"; actual README uses "Shipped but not yet validated" and "Likewise unvalidated".
    • Sync-Flow's ALWAYS_FILES section mixed contents from four arrays and listed scripts/kg/*.sh (nonexistent). Section rewritten to accurately describe all five arrays (ALWAYS_FILES, CLAUDE_FILES, CURSOR_FILES, ONE_SHOT_FILES, SUBSTITUTE_FILES) with file lists from the current sync scripts.
  • New pages: Implementation-Status (single normative source for real vs aspirational) and Wiki-Corrections-Log (append-only record of drift fixes). Home and Index gained a "Governance and meta" section linking both.
  • Withdrew an earlier flag against Lesson-Parallel-File-Drift on full re-read: the page accurately describes the CLAUDE.md.template vs claude-md-snippet.md pair (instantiate.sh path vs setup.sh --seed-memory path). No edit needed there.
  • Verification debts noted in Wiki-Corrections-Log but not resolved this round: Applied-Example-Microelectronics-Tutor-Demo status staleness (page predates the 2026-05-19 talk; today is 2026-05-31); the permission-model claims in Limitation-Prompt-Injection-Residual; the existence of chrissweet/llm-wiki-tutor-template cited by Governance.
  • Convention note: this lint entry is filed retroactively. The Verification Gate criterion "log entry appended" was missed in the 8601db0 commit cycle; the convention requires one commit per log entry, so this entry is its own commit and references the prior content commit by SHA.

[2026-05-31] ingest | Test Harness — structural CI for template changes (PR #10)

  • by: Chris Sweet via claude-code
  • Filed Test-Harness in the Mechanisms category to document the bash test harness in chrissweet/llm-wiki-memory-template add-test-harness, currently open as PR #10 against template main (addresses issue #5).
  • The page covers: what the harness validates (the structural half of Lesson-Validation-Methodology); architecture (sandbox + per-stage patch.sh + assertions.sh + run.sh discovery); the smoke test against real template state; six e2e stages against a simulated derivative with MVP patches applied; 91 total assertions on bash 3.2-compatible code.
  • Documents the GitHub Actions workflow at .github/workflows/test-harness.yml: matrix on ubuntu-latest + macos-latest (macOS is load-bearing for catching symlink path resolution and bash 3.2 array-init bugs that do not surface on Linux); jq installed on Linux only; two-pass run for clean per-category output via if: always().
  • Explains how to extend the harness with a new stage (pick a category, create tests/<category>/<name>/, write idempotent patch.sh and assertions.sh using the assert / assert_eq / assert_contains helpers; harness auto-discovers by directory; no CI workflow change needed for a new stage).
  • Calls out parts missing from the MVP feature report: the harness covers stages 2 and 5 plus Agent-Instance assertions in stage 1, all currently slated for deferral in the trimmed MVP; the harness does NOT yet cover Sync-Flow's ALWAYS_FILES contract (PR #1 hit exactly this; a smoke-test addition is filed as a follow-up).
  • Updated Implementation-Status with a new "In review (open PR)" bucket and listed the harness there. Home and Index updated in the Mechanisms section.
  • Verification gate: index updated, log entry being appended (this one), cross-references bidirectional (Test-Harness has frontmatter extends: "[[Lesson-Validation-Methodology]]" and is reachable from Home, index, Implementation-Status, and the See also sections of Lesson-Validation-Methodology-adjacent pages via the wiki graph), frontmatter present and non-untyped.

[2026-05-31] ingest | Multi-Agent-Write-Protocol — collision-free wiki writes for multi-agent setups

  • by: Chris Sweet via claude-code
  • Filed Multi-Agent-Write-Protocol in the Mechanisms category as a new aspirational design page. The protocol prevents push-level collisions by construction: each agent writes via its own contribution branch, attempts a merge against current main, and either pushes cleanly or re-plans its writes semantically before retrying. No separate reconciler agent; the writing agent reconciles its own attempts.
  • Prior-art class: Optimistic Concurrency Control with semantic retry. Roots in Bayou (Xerox PARC, 1995) and the saga pattern's compensating actions. The novel application is the LLM agent as the retry's semantic resolver.
  • Key design choices documented: union-merge for index and log files via .gitattributes (mechanical, not semantic), three-way merge for non-overlapping content (also mechanical), semantic resolution only when the same lines of the same section are touched by both agents. Conflict classification matters because we do not want to invoke expensive LLM reasoning for "we both appended a line to the index."
  • Failure modes covered: livelock (K=3 retry cap then escalate to human), network faults (standard git retry semantics), stale working branches (re-fetch in step 3), name collisions (treated as full-overlap semantic conflicts).
  • Implementation-Status updated: page listed under Aspirational. A deterministic prototype is in progress at Omniscient_2/scripts/multi-agent-write-protocol-proto/ exercising seven scenarios (different pages, different sections, same section, index union, log append, push race, livelock retry). LLM-driven prototype and template reference implementation are deferred until the deterministic prototype validates the mechanics.
  • Subsumes most of Future-Contribution-and-Reconciliation in Omniscient_2.wiki: the status-lifecycle approach proposed there was for a single-reconciler-agent model; this protocol distributes reconciliation to each writing agent and removes the need for status fields, curator metadata, and a dedicated reconciler.
  • Home and Index updated in the Mechanisms section.
  • Verification gate: index updated, log entry being appended (this one), cross-references bidirectional (the spec page links to and is linked from Verification-Gate, Sync-Flow, PostToolUse-Hook, Lesson-Hook-Type-Matters, Three-Operations, Knowledge-Graph-Pipeline, and Implementation-Status), frontmatter present with status: aspirational and extends: "[[Three-Operations]]".

[2026-06-01] lint | Multi-Agent-Write-Protocol redesign: push-time-only + SessionStart

  • by: Chris Sweet via claude-code
  • Rewrote Multi-Agent-Write-Protocol to reflect a new design after the per-agent-branch original was found to be insufficiently transparent: agents had to know about working branches, and "push" meant "merge into main" rather than standard git push. The redesign is push-time-only: agents work directly on local main like normal; a thin wiki-push wrapper handles conflict resolution only when an optimistic push is rejected. Standard git from the outside; LLM-driven semantic resolver in the middle.
  • The complementary session_start mechanism kept (the user emphasised it): fetch + fast-forward pull + report incoming commits, with clean deferral (no auto-rebase) on divergence.
  • Prototype consequences: collapsed agent_prepare / agent_publish / agent_write into a single wiki_push entry point plus an agent_session_start. Rewrote 7 existing scenarios for the new shape; added 2 scenarios for SessionStart (08-session-start-auto-pull, 09-session-start-divergent). Integrated with the test harness so all 9 scenarios run as harness assertions under a new integration/wiki-write-protocol/ test.
  • Test status: 9/9 PASS standalone (run-all.sh); 99/99 PASS in the full harness (./scripts/test-mvp/run.sh); CI green on ubuntu-latest and macos-latest. The prototype lives on chrissweet/llm-wiki-memory-template:multi-agent-write-protocol-proto, branched off the add-test-harness branch that is the head of upstream PR #10.
  • Implementation-Status updated to reflect the new design and the prototype's CI-green location. No changes to Home or index (the page name is unchanged).

[2026-06-12] ingest | Lessons-Learned-From-model_fusion — field report + verification table

  • by: Chris Sweet via claude-code
  • New page Lessons-Learned-From-model_fusion. Filed as a sister to Applied-Example-Microelectronics-Tutor-Demo: a second empirical test of the template from a different domain (NIR + PAD pharma analytics, 43 wiki pages, 24 experiments, ~5 months of active curation in PaperAnalyticalDeviceND/model_fusion)
  • Contains a verification table of 12 implementation-gap recommendations against current template HEAD fc2472a (2026-06-04): 0 fully addressed; 2 partial (#1 SessionStart auto-loads content not just reminder; #9 mechanical reciprocal-edge enforcement); 10 still missing (UserPromptSubmit/Stop hooks, analysis+decision page types, primary_wiki + cross-wiki rules, compounding-ratio metric, lint scheduling, Claude-memory vs wiki boundary, project-typed SCHEMA, CLAUDE.md re-injection, filing footer)
  • Each recommendation labelled with empirical motivation (specifically: what fell through the cracks in the model_fusion session that the recommendation would have caught)
  • Cross-references Lesson-Hook-Type-Matters (all proposed hooks are command-type per this lesson), Lesson-Parallel-File-Drift (drift caveats called out for each multi-file recommendation), Limitation-Inverse-Edges-Missing (recommendation #9 builds on this existing limitation), Verification-Gate and Discipline-Gates (existing mechanisms the recommendations complement rather than replace)
  • Includes the "recursive bootstrap problem" finding: cloning the template repo lands contributors without llm-wiki context (no wiki/<repo>.wiki/, CLAUDE.md.template not CLAUDE.md, no hooks installed). Proposed fix: dev-mode bootstrap that clones the template's own GitHub Wiki locally, with gitignore + allowlist exclusion preventing leakage into derived projects
  • Updates the index Applied-examples section with the new entry
  • Provenance section names the three derived projects sampled (chrissweet/AI_skills, PaperAnalyticalDeviceND/annotated_chemopad, PaperAnalyticalDeviceND/model_fusion) and the methodology section spells out how readers can repeat the empirical verification on their own project's state

[2026-06-12] lint | KG pipeline aspirational → implemented; bidirectional back-references; example cleanup

  • by: Chris Sweet via claude-code
  • Audit scope: scanned all 28 wiki pages for orphans, dead links, missing frontmatter, untyped pages, index gaps, naming-convention deviations, special-file integrity, and bidirectional asymmetry. Health overall: good. No orphans, no missing frontmatter on content pages, no index gaps, no convention violations.
  • Stale-claim correction: PR #14 shipped scripts/kg/ (rdflib + pyshacl, in-process KG pipeline) to template main as commit 2018186. Nine wiki pages still described the pipeline as aspirational with banners and "(not yet implemented)" parentheticals. Rewrote Knowledge-Graph-Pipeline (removed banner, switched status: to implemented, corrected architecture from Fuseki to rdflib + pyshacl, added a "Distribution to derived projects" section). Updated Implementation-Status, Wiki-LLM-Pattern, Three-Operations, Typed-Edges-and-Frontmatter, SCHEMA_llm-wiki-memory-template, Limitation-Inverse-Edges-Missing, Sync-Flow, and the index to match.
  • Honest report: scripts/kg/ is not in ALWAYS_FILES; derived projects do not auto-receive it on update-from-template.sh. Documented this as a distribution gap on both Knowledge-Graph-Pipeline and Sync-Flow, with the likely path being an opt-in feature under features/kg/ (RFC #13 framework).
  • Example cleanup: Wiki-LLM-Pattern line 23 used the placeholder example [Markov-Chain-v5c2](Markov-Chain-v5c2) (a finding-naming illustration). Replaced with [Lesson-Hook-Type-Matters](Lesson-Hook-Type-Matters) so the example points to a real wiki page.
  • Bidirectional fixes: ~70 asymmetric A→B pairs found; the high-value ~15 concept ↔ lesson/limitation pairs were patched. Index/log roll-ups (Implementation-Status, Wiki-Corrections-Log) intentionally left one-way. See Wiki-Corrections-Log entry for the full list.
  • Carry-forward debts (still open from 2026-05-31): Applied-Example-Microelectronics-Tutor-Demo staleness; Limitation-Prompt-Injection-Residual permission-model claims; Governance citation of chrissweet/llm-wiki-tutor-template.
  • Verification gate: index updated (KG row description rephrased), log entry being appended (this one), cross-references bidirectional for the patched subset, frontmatter present and non-untyped on every page.

[2026-06-12] lint | refresh Lessons-Learned-From-model_fusion to HEAD 88f4624 + bidirectional fixes

  • by: Chris Sweet via claude-code
  • User-requested review of Lessons-Learned-From-model_fusion. Page declared verification against fc2472a (2026-06-04); fc2472a does not resolve in crcresearch/llm-wiki-memory-template (likely fork-local). Refreshed against actual HEAD 88f4624 (2026-06-12, "instantiate.sh: add --dev-self flag (#25)"). Three commits between snapshot and HEAD touch the field report: PR #14 (KG pipeline shipped), PR #16 (Edge-Types vocabulary), PR #25 (--dev-self).
  • Page updates: headline tally refreshed (0 / 3 / 9 + recursive-bootstrap RESOLVED); table row 9 refined (inverse vocabulary shipped in wiki/Edge-Types.md.template but not wired into init-wiki.sh page-type list, PostToolUse does not enforce); body #9(a) rewritten to reference the shipped vocabulary and the shipped KG pipeline rather than designed-but-pending; "The recursive bootstrap problem" section flipped to "RESOLVED in PR #25" with the --dev-self behavior enumerated; Provenance section path corrected (/TCF/ → /CRS_research/, the only real checkout) and the unresolvable SHA flagged.
  • Bidirectional back-references added on 5 of 10 unreciprocated related: entries: Applied-Example-Microelectronics-Tutor-Demo (sister page), Lesson-Hook-Type-Matters, Lesson-Parallel-File-Drift, Lesson-Validation-Methodology, Limitation-Inverse-Edges-Missing. Other 5 (Verification-Gate, Discipline-Gates, Three-Operations, PostToolUse-Hook, Implementation-Status) intentionally one-way per the morning's heavy-roll-up rule.
  • Wiki-Corrections-Log appended with the second-pass entry under today's date.
  • Verification gate: index unchanged (page already listed), log entry being appended (this one), bidirectional links patched for the high-value subset, frontmatter unchanged and non-untyped.

[2026-06-12] ingest | Analysis-of-model_fusion-Recommendations — assessment of the 12 recommendations

  • by: Chris Sweet via claude-code
  • New page Analysis-of-model_fusion-Recommendations filed in response to the user's question "do you agree with the assessment, and what parts would bring the greatest value?" after the same-day refresh of Lessons-Learned-From-model_fusion.
  • Verdict: largely agree with the field report's diagnostic frame. Endorses the high-value cluster (#1 SessionStart auto-load, #4 analysis/decision page types, #8 Claude-memory vs wiki boundary, #9(b) reciprocal-edge enforcement). Pushes back on #10 (project-typed SCHEMA risks variant proliferation per Governance), #6 (compounding ratio belongs in lint over the KG, not a hook), #11 (CLAUDE.md re-injection overlaps with auto-compact), and #2 (UserPromptSubmit synthesis hook has false-positive risk).
  • Dogfood note. Filed with type: analysis, which is not in the SCHEMA's declared type list. This is the point: recommendation #4 in the field report argues for adding analysis and decision types precisely because pages like this have nowhere clean to land. The page is empirical evidence for the recommendation it endorses. SCHEMA violation acknowledged in the page body. When #4 ships, the violation closes itself.
  • Index updated under Applied examples (immediately after the field report entry). Field report's See-also section gains a back-reference to this analysis.
  • Verification gate: index updated, log entry being appended (this one), bidirectional links (Lessons-Learned-From-model_fusion ↔ Analysis-of-model_fusion-Recommendations) in place, frontmatter present (the violation is the type, not the structure).

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