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Harden chart node data, rendering, and lifecycle - #9
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…27) Two related documentation cleanups. Document the branch/PR/merge workflow. CONTRIBUTING.md covered PR content expectations but never described branching or merge mechanics, even though the commit history has followed a consistent convention for 26 PRs. Writes down what was already practice: topic branches off main, agent/<slug> naming, push, PR via the existing template, squash-merge, delete branch. Also corrects README.md, which still claimed a GitHub Actions workflow runs a compile check on every push - that automation was removed in 185143a, so local validation is now the only gate. Remove references to gitignored planning docs. 65 tracked files carried 79 citations like "see doc/ARCHITECTURE_REVIEW_FINDINGS.md #9". Because doc/ is gitignored, these were dead links for anyone reading the repo, exposed the internal doc names and their finding/section numbering, and replaced the actual rationale with a lookup key - so the reader most likely to need the reasoning could not reach it. Each citation is replaced with the substance it pointed at, stated inline. Comments and docstrings only; no behavior change. Verified: python -m compileall passes, full suite 486 passed. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
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Settings' General page had a Theme select (Dark/Muted/Monochromatic) that persisted a real setTheme intent, but nothing in the SPA ever applied the value: no data-theme attribute, no alternate --gl-surface-* token set, the app rendered identically regardless of selection. Per user decision, removed rather than wired up - building two real alternate palettes is a design investment, not a bug fix, and a persisted preference that provably does nothing is worse than no preference. Removed end to end: the frontend select and its options, the setTheme intent and its handler, get_theme/set_theme on SettingsManager (including the now-pointless in-memory backfill for legacy state files missing the key), the theme field from the app-settings wire contract (regenerated), and the now-stale "Appearance" Help entry that described this exact control. Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
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Summary
This PR repairs chart/graph-node data integrity, rendering behavior, graph lifecycle handling, and persistence.
What changed
Root cause
Chart data rules were duplicated between the agent, scene item, renderer, and persistence layers. Async insertion relied on the current node as a fallback, and charts were represented as loosely attached content without stable graph lifecycle metadata.
Validation
python -m pytest -q