.memex/
├── config.json   — configuration (thresholds, decay rates)
├── index.md      — L1 memory index (always loaded, ~50-80 lines)
├── topics/       — L2 topic files (loaded on-demand, <100 lines each)
└── archive/      — L3 JSON entries (full metadata, searchable)

src/
├── cli.ts                  # CLI entry point (commander.js)
├── core/
│   ├── schema.ts           # MemoryEntry types, validation, factories
│   ├── store.ts            # CRUD for L3 archive (atomic JSON writes)
│   ├── tiers.ts            # L1/L2 tier management (markdown files)
│   └── index.ts            # Index builder (L1 generation from L2/L3)
├── algorithms/
│   ├── scoring.ts          # Effective score: confidence × access × decay
│   ├── dedup.ts            # Jaccard similarity + 4-op model
│   ├── decay.ts            # Half-life decay calculator
│   └── promote.ts          # Tier promotion/demotion logic
├── llm/
│   ├── extract.ts          # LLM-powered memory extraction from transcripts
│   └── consolidate.ts      # LLM-powered merge and dedup
├── exporters/
│   ├── claude.ts           # CLAUDE.md + MEMORY.md export
│   ├── cursor.ts           # .cursor/rules/*.mdc export
│   ├── aider.ts            # CONVENTIONS.md export
│   └── agents-md.ts        # AGENTS.md universal export
├── hooks/
│   ├── claude-code.ts      # Claude Code hook handlers
│   ├── mcp-server.ts       # MCP server mode (JSON-RPC over stdio)
│   └── generic.ts          # Generic transcript extraction
├── scanner/
│   ├── patterns.ts         # Built-in ast-grep/semgrep patterns (TS, Python, Go, Rust)
│   ├── scanner.ts          # Code scanning engine (ast-grep + semgrep backends)
│   └── validator.ts        # Memory validation against code
├── bench/
│   ├── locomo.ts           # LoCoMo dataset loader
│   ├── runner.ts           # Benchmark execution engine
│   ├── evaluator.ts        # F1 scoring + metrics
│   ├── baselines.ts        # Baseline implementations (+ scan baseline)
│   └── report.ts           # Results formatting
└── commands/
    ├── init.ts, status.ts, add.ts, search.ts
    ├── audit.ts, prune.ts, export.ts, scan.ts, validate.ts
    ├── consolidate.ts, extract.ts, bench.ts, serve.ts
tests/
    ├── schema.test.ts      # 9 tests
    ├── store.test.ts       # 13 tests
    ├── scoring.test.ts     # 6 tests
    ├── dedup.test.ts       # 15 tests
    ├── decay.test.ts       # 11 tests
    ├── tiers.test.ts       # 19 tests
    ├── exporters.test.ts   # 9 tests
    └── commands.test.ts    # 6 tests (CLI integration)

effective_score = confidence × max(1, log2(access_count + 1)) × decay_factor

memex init [--claude] [--force]      Initialize .memex directory
memex status                         Dashboard with health metrics
memex add <text> [options]           Add a memory entry
  --category <cat>                     pattern|decision|gotcha|preference|project|tool
  --tags <tags>                        Comma-separated tags
  --confidence <n>                     0.0-1.0 (default: 0.7)
memex search <query> [options]       Fuzzy search across tiers
  --category <cat>                     Filter by category
  --limit <n>                          Max results (default: 10)
memex audit [--json]                 Score and flag entries
memex prune [options]                Remove low-scoring entries
  --threshold <n>                      Score threshold (default: 0.1)
  --dry-run                            Preview without removing
  --hard                               Permanently delete (vs archive)
memex export [options]               Export to tool formats
  --claude / --cursor / --aider / --agents-md / --all
memex consolidate [--dry-run]        LLM-powered merge (needs API key)
memex extract [options]              Extract from transcripts (needs API key)
  --from-stdin                         Read from stdin (hook mode)
  --file <path>                        Read from file
  --trigger <event>                    pre-compact|stop|session-end
memex bench [options]                Run LoCoMo benchmark
  --quick                              2 conversations only
  --baselines <list>                   Comma-separated baselines
  --ci --threshold <n>                 CI mode with F1 threshold
memex scan [dir] [options]          Scan codebase for conventions
  --backend <backend>                  ast-grep | semgrep | auto
  --lang <languages>                   Comma-separated languages
  --min-matches <n>                    Minimum matches to report
  --dry-run                            Preview without saving
  --benchmark                          Compare ast-grep vs semgrep
memex validate [dir] [options]      Validate memories against code
  --backend <backend>                  ast-grep | semgrep | auto
  --json                               Machine-readable output
memex serve                          Start MCP server (stdio)