Code graph

The graph pane's Code view shows this repository as a rotating sphere of files and symbols, lit as coding agents search and read it. The index behind it is codebase-memory-mcp, the same MCP server that Codex and Claude Code sessions use to understand the codebase.

Upstream	DeusData/codebase-memory-mcp
Pinned	0.10.8, installed unmodified
License	MIT
Upstream checked 2026-10-19	v0.12.1 (2026-10-16), two minor releases ahead

Why codebase-memory-mcp

It already builds a code knowledge graph with a native 3D layout endpoint and serves it to agents over MCP. Obsidience shows that one index instead of building a second parser, graph store or layout: agents and the owner look at the same graph, and every lookup an agent makes lights the nodes it returned.

Flow

flowchart LR
  subgraph Provider["codebase-memory-mcp (obsidience-code-graph.service)"]
    daemon["Permanent daemon<br/>index and viewer"]
    layout["/api/layout"]
  end
  agents["Codex and Claude Code<br/>MCP sessions (analysis profile)"] -->|"join the daemon"| daemon
  agents -->|"tool receipts in<br/>local journals"| activity["Agent activity listener<br/>graphs/agent_activity.py"]
  saves["Saved files in the repository"] --> activity
  activity -->|"file events"| refresh["Coalesced refresh<br/>graphs/code_refresh.py"]
  refresh -->|"index_repository"| daemon
  adapter["Code graph adapter<br/>graphs/codebase.py"] -->|"layout read"| layout
  route["GET /api/graphs/code"] --> adapter
  activity -->|"operations with<br/>returned identities"| ws["/ws/activity"]
  route --> ui["Graph pane, Code view<br/>ui/.../graph/code"]
  ws --> ui

• The service keeps the provider's permanent daemon and graph viewer running. It starts before restored agent sessions, because a daemon spawned by an agent's MCP session stops with its last session. Agent sessions join it with the read-only analysis tool profile; nothing else starts a second owner.
• The adapter reads the native layout, maps stable qualified names to compact display identities, and adds bounded in-repository SHA-256 fingerprints of each symbol's saved source span (never source text) so the view can tell which symbols changed.
• The refresh coalesces saved-file events for 750 ms into one native index_repository pass; a failed refresh shows the snapshot as stale.
• The activity listener turns new tool calls in the local Codex and Claude Code journals into fixed operation labels and the identities they returned, without reasoning, source or command output. Of a call's arguments only the lookup's tool and search terms (and a trace's direction and depth) pass; the Code stage shows the newest lookup as a card in the graph labels' style while its nodes are lit.

Boundary

File	Owns
harness/graphs/codebase.py	The one connection to the provider: URL and project settings, the layout client, refresh and activity lifecycles, the display projection
harness/graphs/code_refresh.py	Coalesced saved-file index refreshes through the provider's CLI
harness/graphs/agent_activity.py	Display-only agent tool receipts and repository file events
harness/interfaces/api/routes/graphs.py	HTTP serialization of the projection
harness/systemd/obsidience-code-graph.service	The provider daemon and viewer
ui/src/renderer/src/graph/code/	The Code view's renderer (spherical layout shared with Knowledge)

The derived index stays outside the Vault and Source; no index artifact enters the repository.

Configuration

Optional keys in obsidience/obsidience.toml:

[graphs]
codebase_url = "http://127.0.0.1:9749"   # the provider's viewer
codebase_project = "home-user-Projects-obsidience"   # default: repository path with "/" replaced by "-"

The view reports unavailable while the provider is absent and never polls.