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Path	Synopsis
apps
backend Package backend wires the app layer to a concrete store.	Package backend wires the app layer to a concrete store.
bundle Package bundle defines the content-bundle serialization format used by pack export/import (file-based CLI) and admin export/import (HTTP).	Package bundle defines the content-bundle serialization format used by pack export/import (file-based CLI) and admin export/import (HTTP).
cli Package cli implements the brainjar command-line interface on top of cobra.	Package cli implements the brainjar command-line interface on top of cobra.
http
middleware
reqctx
server Package server implements the brainjar HTTP server.	Package server implements the brainjar HTTP server.
mcp
server Package server builds the brainjar MCP server.	Package server builds the brainjar MCP server.
tools Package tools holds the brainjar MCP tool implementations.	Package tools holds the brainjar MCP tool implementations.
models
platform Package platform adapts brainjar's composed prompts to agent-specific config files on disk.	Package platform adapts brainjar's composed prompts to agent-specific config files on disk.
adapterkit Package adapterkit holds the helpers shared by every brainjar Platform adapter: marker constants, brainjar brand strings, atomic file / JSON I/O, hook-entry identity, and the managed-section merge algorithm.	Package adapterkit holds the helpers shared by every brainjar Platform adapter: marker constants, brainjar brand strings, atomic file / JSON I/O, hook-entry identity, and the managed-section merge algorithm.
claude Package claude is the brainjar Platform adapter for Claude Code.	Package claude is the brainjar Platform adapter for Claude Code.
codex Package codex is the brainjar Platform adapter for OpenAI Codex CLI.	Package codex is the brainjar Platform adapter for OpenAI Codex CLI.
cursor Package cursor is the brainjar Platform adapter for the Cursor IDE (cursor.com).	Package cursor is the brainjar Platform adapter for the Cursor IDE (cursor.com).
testutil Package testutil provides shared test contracts that every platform adapter runs against.	Package testutil provides shared test contracts that every platform adapter runs against.
secrets Package secrets resolves an api_key_ref (e.g.	Package secrets resolves an api_key_ref (e.g.
stores
sqlite
updater Package updater implements `brainjar upgrade` — in-process self-update that fetches the latest release from R2, verifies the cosign bundle against a pinned identity, and atomically swaps the running binary.	Package updater implements `brainjar upgrade` — in-process self-update that fetches the latest release from R2, verifies the cosign bundle against a pinned identity, and atomically swaps the running binary.