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SecondBrain & Memory System — URL Reference Catalogue

Every URL researched as inspiration for PKA's knowledge architecture

Date: 2026-04-15  |  MC-602

42
URLs Catalogued
20
Adopted / Influenced
8
Sections
4
Non-URL Refs

1. Karpathy LLM Wiki Pattern FULLY ADOPTED

Most influential single reference. PKA independently built the same 3-layer architecture (raw sources → wiki layer → schema layer). Formally adopted in MC-605.

URLDescriptionFinding / Impact
gist.github.com/karpathy/442a6bf... Karpathy LLM Wiki Gist Personal knowledge system: raw sources → wiki → schema. PKA had 12/12 core patterns already implemented. adopted
x.com/karpathy/status/203980... Karpathy Tweet Thread Original announcement of the LLM Wiki concept. Validated PKA's approach. adopted

2. GitHub Repositories — SecondBrain Templates

Evaluated March 2026. Five repos reviewed for patterns and skills to adopt.

URLDescriptionFinding / Impact
github.com/bradautomates/second-brain Brad's Second Brain Template Brain dump workflow, auto-commit hooks, delegation patterns. Adopted: /brain skill, "grep before glob" principle, auto-commit, git-as-database. adopted
github.com/earlyaidopters/second-brain Early Adopters Second Brain Setup scripts, Gemini file import, beginner template. Less relevant for PKA's maturity level. reviewed
github.com/kepano/obsidian-skills Kepano's Obsidian Skills (Obsidian CEO) 5 skills: obsidian-markdown, obsidian-bases, json-canvas, obsidian-cli, defuddle. All installed globally. adopted
github.com/coleam00/second-brain-skills Cole's Second Brain Skills MCP client wrapper, PPTX generation, brand voice. Influenced "progressive disclosure" pattern (metadata in context, body on trigger). influenced
github.com/Abilityai/cornelius Zettelkasten Automation FAISS search, brain swapping. Too complex; A-MEM paper covers concepts better. reviewed

3. Production Memory Frameworks

Evaluated April 2026 (MC-539). Eight production-grade memory systems compared against PKA's approach.

URLDescriptionFinding / Impact
github.com/garrytan/gbrain Garry Tan's GBrain Markdown + pgvector hybrid, compiled truth + timeline pages, dream cycles. High influence: adopted compiled truth pattern and dream cycle concept. adopted
github.com/letta-ai/letta Letta (MemGPT) OS-inspired tiered memory with agent paging between tiers. Sleep-time compute concept influenced vault tiered architecture. influenced
github.com/mem0ai/mem0 Mem0 Production Memory Universal memory layer (186M API calls/quarter). 26% accuracy improvement benchmark. Not adopted — API dependency reduces inspectability. reviewed
github.com/langchain-ai/langmem LangChain Memory SDK Semantic + episodic + procedural taxonomy. Good reference but too coupled to LangChain ecosystem. reviewed
github.com/microsoft/graphrag Microsoft GraphRAG LLM builds entity knowledge graphs. Decided against: graph database overhead not justified for single-user agent. reviewed
github.com/getzep/graphiti Zep Graphiti Temporal knowledge graphs, 94.8% DMR benchmark. Bi-temporal concept interesting but complex. reviewed
github.com/agiresearch/A-mem A-MEM Agentic Memory Zettelkasten-inspired memory with linked notes and memory evolution. High influence: new facts update old memories. SOTA on 6 models. adopted
github.com/modelcontextprotocol/.../memory MCP Memory Server Official MCP knowledge graph server. Reviewed as integration point; vault_mcp.py provides similar functionality natively. reviewed

4. Academic Papers

Theoretical grounding for memory architecture. 13 papers reviewed, 5 with high influence on design.

URLDescriptionFinding / Impact
arxiv.org/abs/2304.03442 Park et al. (2023) — Generative Agents Foundational. Memory stream + reflection + planning. "Reflection was single biggest contributor to believable behavior." Retrieval: recency × importance × relevance. foundational
arxiv.org/abs/2310.08560 Packer et al. (2023) — MemGPT OS-inspired tiered memory. Influenced vault architecture (working/short-term/long-term tiers). influenced
arxiv.org/abs/2305.10250 Zhong et al. (2023) — MemoryBank Ebbinghaus forgetting curves for AI memory. Influenced stale_after and memory health tracking. influenced
arxiv.org/abs/2308.15022 Wu et al. (2023) — Recursive Summarizing for Dialogue Hierarchical compression algorithm. Relevant for dream cycle "merge" operations. reviewed
arxiv.org/abs/2502.12110 Xu et al. (2025) — A-MEM Agentic Memory High influence. Zettelkasten for agents. Memory evolution: new facts trigger updates to old memories. SOTA on 6 models. adopted
arxiv.org/abs/2502.06975 Pink et al. (2025) — Episodic Memory for Long-Term Agents Tulving's episodic/semantic distinction. Consolidation pathway (episodic → semantic) = dream cycle concept. influenced
arxiv.org/abs/2504.13171 Lin et al. (2025) — Sleep-time Compute Key paper. Academic foundation for dream cycles. ~5x compute reduction, 13-18% accuracy improvement. From MemGPT founders. foundational
arxiv.org/abs/2504.19413 Chhikara et al. (2025) — Mem0 Scalable Long-Term Memory Production benchmark: 26% accuracy improvement, 91% lower latency, 90% cost savings. reviewed
arxiv.org/abs/2404.13501 Zhang et al. (2024) — Memory Mechanism Survey 39-page taxonomy. Three dimensions: sources, forms, operations. reviewed
arxiv.org/abs/2512.13564 Hu et al. (2025) — Memory in the Age of AI Agents Most comprehensive survey (47 authors). Broad landscape view. reviewed
arxiv.org/abs/2404.16130 Edge et al. (2024) — Graph RAG: Local to Global Microsoft's graph RAG paper. Reviewed but not adopted — too heavyweight for our scale. reviewed
arxiv.org/abs/2501.13956 Rasmussen et al. (2025) — Zep Temporal Knowledge Graphs Bi-temporal model. Good concept but complex implementation. reviewed
arxiv.org/abs/2501.01880 Li et al. (2025) — Long Context vs. RAG Validated our approach: at small corpus size, long context wins over RAG. FTS5 as hedge for growth. foundational

5. Expert Commentary & Blog Posts

Industry analysis that shaped architectural decisions. 13 posts from leading AI practitioners.

URLDescriptionFinding / Impact
anthropic.com/.../effective-context-engineering... Anthropic Engineering Core philosophy. "Smallest set of high-signal tokens." Keep memory lean. Directly influenced markdown-as-source-of-truth. foundational
mem0.ai/blog/state-of-ai-agent-memory-2026 Mem0 Blog — State of AI Agent Memory 2026 Comprehensive 2026 overview. Positioned PKA within the landscape. Validated file-based memory as mainstream. reviewed
letta.com/blog/agent-memory Letta Blog — Agent Memory Deep Dive Tiered memory concepts. Useful framing for working/short-term/long-term tiers. reviewed
huyenchip.com/2025/01/07/agents.html Chip Huyen — "Agents" Context Expansion Law: context expands to fill limits, so RAG stays relevant. Important contrarian view. influenced
hamel.dev/notes/llm/rag/not_dead.html Hamel Husain — "Stop Saying RAG Is Dead" RAG economics still matter. Graph DBs unnecessary. ColBERT > single-vector. reviewed
simonw.substack.com/.../things-we-learned... Simon Willison — "Things We Learned About LLMs in 2024" Long inputs > short prompts, but keep infra simple. Validated SQLite-everything philosophy. influenced
jxnl.co/.../facets-context-engineering/ Jason Liu — "Beyond Chunks: Context Engineering" Faceted search with structured extraction > top-k vector search. Influenced YAML frontmatter approach. influenced
sequoiacap.com/.../harrison-chase/ Harrison Chase (LangChain) — Sequoia Podcast Key quote: "If you're building a long-horizon agent, give it access to a file system." Validated file-based approach. foundational
cognition.ai/blog/devin-annual-performance-review-2025 Cognition — Devin Annual Review 2025 DeepWiki reference. Proprietary code-specialized indexing. Enterprise-grade but closed-source. reviewed
ragflow.io/blog/rag-review-2025-from-rag-to-context RAGFlow — "2025: From RAG to Context" RAG evolution overview. Context engineering superseding pure retrieval. reviewed
alexgarcia.xyz/.../sqlite-vec-hybrid-search/ Alex Garcia — Hybrid Search with SQLite FTS5 + sqlite-vec hybrid. Shows SQLite can do hybrid without Postgres. influenced
glaforge.dev/.../reciprocal-rank-fusion/ Guillaume Laforge — Reciprocal Rank Fusion RRF technical reference. Relevant if we add hybrid retrieval later. reviewed
dev.to/imaginex/.../markdown-files-all-you-need ImagineX — "Markdown Files Are All You Need" Community validation of our exact approach. Markdown files as complete memory solution. influenced

6. YouTube & Community References

Video content and community discussions that influenced design decisions.

URL / SourceDescriptionFinding / Impact
youtu.be/mi4hcipESKQ Nate Herk — Claude Code EA Claude Code as Executive Assistant. Influenced assistant/dispatch model. influenced
Greg Isenberg / Vin (212K views) Thinking Tools & Second Brain Philosophy /ghost, /challenge, /trace, /connect, /ideas patterns. "Writing and daily reflection are the engine." Phase 2 thinking tools conceptualized. influenced
Mark Kashef (YouTube) Obsidian Skills & Session Summary Workflows Led to installing kepano/obsidian-skills. /tldr concept influenced session indexer. adopted
Brad (bradautomates, YouTube) Brain Dump & Git Philosophy Brain dump auto-classify, auto-commit hooks, grep-before-glob. Multiple patterns adopted into /brain skill. adopted
Cole (coleam00, YouTube) Progressive Disclosure Pattern "Metadata always in context, body when triggered, resources as needed." Adopted in skill architecture. adopted

7. Key Decisions Made From Research

Adopted

Explicitly Rejected

8. Summary

CategoryCountAdopted/Influenced
Karpathy LLM Wiki2 URLs2 fully adopted
GitHub Templates5 URLs3 adopted
Memory Frameworks8 URLs3 influenced
Academic Papers13 URLs5 high-influence
Expert Commentary13 URLs4 directly shaped
YouTube / Community1 URL + 4 refs3 led to adoptions
TOTAL 42 URLs + 4 refs 20 adopted/influenced

Generated by Luci  |  MC-602  |  2026-04-15