Color Coding
Color coding is a cross-cutting layer. The same entity carries the same provenance no matter which mode you view it in, so Ship of Tools renders that provenance uniformly across all modes — in the design, a stale annotation looks stale in every mode, because staleness belongs to the entity, not to the view. Built today, staleness is a property of a file and shows on that file's row in Files mode.
Color and badging are orthogonal to mode. A mode decides what tree to show; the color layer decides how each node is tinted based on who touched it, when, and whether its annotation still matches the code.
Design vs. built today
This page describes the cross-cutting colour layer as designed. What renders today is the per-session agent work-state colour (idle · working · blocked · waiting · done, on the Sessions strip and nav rows) and the stale-annotation drift badge, which is per file (the file's content hash against the annotation's synced_against) and shows on the selected file row in Files mode. The per-entity provenance states in the table below — user-edited, agent-edited accept/reject, immutable/external, favorited — are planned. A pinned file already renders, as a bright cyan row in the navigation tree rather than an accented border.
The states
| State | Appearance | Meaning |
|---|---|---|
| User-edited recently | Warm color, fades over time | You touched this entity lately; the warmth decays as it ages. |
| Agent-edited, unaccepted | Distinct color (unresolved diff) | An agent changed this and you have not yet accepted or discarded the change. |
| Agent-edited, accepted | Neutral, small sigil | An agent's change that you accepted; marked with a small sigil but otherwise neutral. |
| Immutable / external | Dimmed | Base, dependencies, vendored code — not yours to edit, rendered dimmed. |
| Stale annotation | Yellowed | The entity's concept annotation was written against an older version of its file (the file's content hash differs from synced_against). Built per file; per-entity staleness is not built. |
| Pinned / favorited | Accented border | You marked this entity for quick return; rendered with an accented border. |
Why it is mode-independent
Provenance is a fact about an entity: who edited it, when, whether its annotation is current. None of those facts change when you switch the root tree from Files to Modules. Encoding them once, at the entity level, means you do not relearn a color scheme per mode — a yellowed badge always means "the prose may not match the code," wherever you see it.
The "stale annotation" state is the direct rendering of the staleness detection described in The Concept Layer: when an annotation's synced_against hash no longer matches the current content hash of its file, the file's row yellows until you refresh it. In the design the same yellow follows the entity into every mode; today it is drawn for the selected file row in Files mode only.