I am using a graph based format which is stored as text file. It is as simple as possible: each node is a line, prefixed with node id, and containing inline node references. I am providing a sample right here:

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[1] *Mind Map Format Overview* - A graph-based documentation format stored as plain text files where each node is a single line. The format leverages LLM familiarity with citation-style references from academic papers, making it natural to generate and edit [3]. It serves as a superset structure that can represent trees, lists, or any graph topology [4], scaling from small projects (<50 nodes) to complex systems (500+ nodes) [5]. The methodology is fully detailed in PROJECT_MIND_MAPPING.md with bootstrapping tools available at https://gist.github.com/horiacristescu/7942db247fdfb31d7150b....

[2] *Node Syntax Structure* - Each node follows the format: `[N] *Node Title* - node text with [N] references inlined` [1]. Nodes are line-oriented, allowing line-by-line loading and editing by AI models [3]. The inline reference syntax `[N]` creates bidirectional navigation between concepts, with links embedded naturally within descriptive text rather than as separate metadata [1][4]. This structure is both machine-parseable and human-readable, supporting grep-based lookups for quick node retrieval [3].

[3] *Technical Advantages* - The format enables line-by-line overwriting of nodes without complex parsing [2], making incremental updates efficient for both humans and AI agents [1]. Grep operations allow instant node lookup by ID or keyword without loading the entire file [2]. The text-based storage ensures version control compatibility, diff-friendly editing, and zero tooling dependencies [4]. LLMs generate this format naturally because citation syntax `[N]` mirrors academic paper references they've seen extensively during training [1][5].

[4] *Graph Topology Benefits* - Unlike hierarchical trees or linear lists, the graph structure allows many-to-many relationships between concepts [1]. Any node can reference any other node, creating knowledge clusters around related topics [2][3]. The format accommodates cyclic references for concepts that mutually depend on each other, captures cross-cutting concerns that span multiple subsystems, and supports progressive refinement where nodes are added to densify understanding [5]. This flexibility makes it suitable as a universal knowledge representation format [1].

[5] *Scalability and Usage Patterns* - Small projects typically need fewer than 50 nodes to capture core architecture, data flow, and key implementations [1]. Complex topics or large codebases can scale to 500+ nodes by adding specialized deep-dive nodes for algorithms, optimizations, and subsystems [4]. The methodology includes a bootstrap prompt (linked gist) for generating initial mind maps from existing codebases automatically [1]. Scale is managed through overview nodes [1-5] that serve as navigation hubs, with detail nodes forming clusters around major concepts [3][4]. The format remains navigable at any scale due to inline linking and grep-based search [2][3].