algometrix_second_brain_builder/CLAUDE.md

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

What This Is

An Obsidian plugin ("Second Brain Builder") that generates detailed explanation notes using Claude Code CLI, Gemini CLI, Codex CLI, or a local Ollama server. Users select text in a note, pick a teaching style (mode), and the plugin spawns the CLI to produce a new note or inline enhancement. Desktop only; supports Windows, macOS, and Linux.

Build Commands

npm install          # install dependencies
npm run build        # type-check (tsc -noEmit) + production bundle
npm run dev          # esbuild watch mode (rebuilds on save)

The build produces main.js (CJS bundle) from the single entry point main.ts via esbuild. Use the Hot-Reload plugin in Obsidian for live dev.

Project Structure

Source lives in src/, bundled to a single root main.js by esbuild (entry point src/main.ts).

• src/main.ts -- ClaudeExplainerPlugin: commands, context menus, the generation queue, CLI/Ollama providers, note orchestration
• src/types.ts -- shared interfaces: modes, inline actions, queue items, settings (+ defaults), provider labels
• src/inline-actions.ts -- the INLINE_ACTIONS catalog (expand, simplify, add diagram, ...)
• src/output-rules.ts -- formatting rules appended to every prompt (getOutputRules, inline/append variants)
• src/cli.ts -- typed child_process.spawn boundary (SpawnedCliProcess, spawnCli)
• src/logger.ts -- in-memory ring logger behind the "Enable logging" setting
• src/utils.ts -- filename sanitizing, JSON array extraction, empty-note detection
• src/ui.ts -- shared modal helpers (title, mode cards, searchable mode grid)
• src/fixers.ts -- output post-processing fixers (code fences, mermaid, callouts, dataview, currency)
• src/modals/ -- one file per modal family: generation.ts, folder.ts, analysis.ts, queue.ts, system-design.ts
• src/settings-tab.ts -- the settings UI, including per-provider setup guides
• modes.json -- note generation modes loaded as BUILTIN_MODES at build time. Gitignored; resolved before every build by scripts/sync-modes.js (from modes.config.json's modesFile if present, else an existing modes.json, else modes.sample.json)
• modes.sample.json -- committed sample set of general-purpose modes (Explain, Deep Inquiry, Feynman, etc.); the default build input for fresh clones
• modes.config.json -- optional, gitignored; { "modesFile": "<path>" } points the build at a personal modes file (conventionally modes.personal.json, also gitignored)
• styles.css -- modal and queue UI styles
• manifest.json -- Obsidian plugin manifest (id: second-brain-builder)
• scripts/ -- build helpers and vault fix scripts:
  • sync-modes.js -- prepares modes.json before builds (see above); wired into npm run build and npm run dev
  • vault-root.js -- shared vault path resolution for the fix scripts (first non-flag CLI argument, OBSIDIAN_VAULT env var, or OBSIDIAN_VAULT= in a gitignored repo-root .env)
  • fix-all.js -- unified runner that executes all fix scripts below in order
  • fix-callout-fences.js -- fixes callout code fences missing the > prefix on closing ``` or content lines
  • fix-currency-dollars.js -- escapes unescaped $ currency signs that Obsidian misinterprets as LaTeX
  • fix-mermaid-end.js -- strips extra end keywords with no matching block opener (subgraph, or sequence-diagram par/alt/opt/loop/rect/critical/break/box) and inserts zero-width space into "end" inside larger words
  • fix-mermaid-missing-end.js -- re-inserts missing end keywords (indentation-based placement) and puts the closing ``` fence on its own line
  • fix-split-end.js -- rejoins lines corrupted by an old regex that split words like "Send" into "S\nend"
  • fix-mermaid-parens.js -- quotes unquoted mermaid node labels containing parentheses or slashes
  • fix-mermaid-quotes.js -- strips nested double quotes inside already-quoted mermaid labels (inner " to ')
  • fix-mermaid-list.js -- fixes "Unsupported markdown: list" errors by converting N./N) to N: in labels and joining - item lines with <br/>

All fix scripts share the same interface: node scripts/<script> <vault-path> for detect-only, add --fix to apply. The vault path can also come from the OBSIDIAN_VAULT environment variable or a gitignored repo-root .env file.

Architecture

Core Flow

1. User selects text, invokes a command (palette or hotkey)
2. A modal (NoteCreatorModal, InlineActionModal, etc.) lets the user pick a mode/action and configure options
3. The plugin builds a prompt by substituting {selection} and {context} placeholders in the mode's prompt template, then appends output rules (getOutputRules() / INLINE_OUTPUT_RULES / APPEND_OUTPUT_RULES)
4. The request is enqueued as a QueueItem (four types: note, inline, append, topic-note)
5. processQueue() processes items sequentially, calling runClaude() which spawns the CLI via child_process.spawn
6. Output goes through five post-processing fixers: fixCodeBlocks, fixMermaidBlocks, fixDetailsBlocks, fixCalloutCodeFences, fixDataviewInlineQueries
7. Result is written to a new note, appended to an existing note, or inserted/replaced inline

Two Command Families

• Note creation ("Explain selection"): creates a new note from selection, replaces selection with a [[wiki-link]]. Uses modes from modes.json + custom user modes. The "Create sub-note" variant splits the selection into multiple topics, generates one note per topic into a named sub-folder of the current note's folder, and injects series instructions so the notes cross-link each other and the parent note.
• Inline actions ("Enhance selection"): transforms selected text in-place (expand, simplify, add examples, add diagram, summarize, challenge, fix & polish, ELI5, translate to code). Defined as INLINE_ACTIONS in main.ts.

AI Provider Abstraction

Supports four backends via settings.aiProvider: "claude" (Claude Code CLI, default), "gemini" (Gemini CLI), "codex" (OpenAI Codex CLI), and "ollama" (local Ollama REST API). The runClaude() method branches on provider: Claude, Gemini, and Codex spawn CLI processes, while Ollama calls /api/generate via Obsidian's requestUrl (non-streaming; requestUrl cannot stream, so the live-output preview fills only for CLI providers). Claude uses --disallowedTools to prevent file writes; Gemini uses --approval-mode plan; Codex uses codex exec --sandbox read-only with the final message captured via --output-last-message written inside the plugin config folder and read back through the vault adapter (its stdout interleaves progress logs; no direct fs usage).

Key Classes

• ClaudeExplainerPlugin (line ~2260) -- main plugin class, owns the queue, status bar, all commands
• NoteCreatorModal -- mode picker for note creation (multi-select, batch generation)
• InlineActionModal -- action picker for inline transformations
• FullNoteActionModal, FillNoteModal, TopicGeneratorModal, FolderGeneratorModal, FolderAnalysisModal, NoteAnalysisModal -- specialized generation modals
• QueueStatusModal -- live progress viewer with retry/remove
• ScaleCalculatorModal, ScaffoldWorkspaceModal -- batch generation utilities
• ClaudeExplainerSettingTab -- plugin settings UI

Output Post-Processing

Generated content is cleaned up before writing to the vault. The fixers (lines ~565-650) handle common LLM output issues: wrapped-in-code-fence removal, mermaid block repairs, <details> to callout conversion, callout code fence prefix fixing, and dataview inline query escaping.

Prompt Template Variables

Mode prompts in modes.json use {selection} and {context} as placeholders. These are string-replaced at enqueue time. Output formatting rules are appended after the mode prompt.

Notes on Output Formatting Rules

The getOutputRules() function defines strict formatting requirements for generated notes: YAML frontmatter first, Title Case headings, no em dashes, short paragraphs, mermaid syntax constraints, Obsidian callout syntax (not HTML <details>). These rules are critical to Obsidian rendering compatibility.