Sources
Grounding, citations, and further reading for System-Prompt Priority Inversion.
All of this is optional. The article itself is self-contained. This page exists so that the referenced GitHub issues are properly cited and so that anyone who wants to trace a specific claim has a direct path to the primary evidence.
Each numbered entry below matches an inline reference in the article. Click any reference number in the article to jump here, or use the back-arrow link on each entry to return.
About the Sources
anthropics/claude-code issue tracker
All four references on this page are user-filed bug reports against the official Claude Code CLI. They are the primary evidence that the documented precedence order (user CLAUDE.md over project CLAUDE.md over skills over system defaults) does not match runtime behavior. Each issue includes reproduction steps, transcripts, and discussion threads with maintainers.
Claude Code memory and CLAUDE.md documentation
The official documentation that states the stated precedence order for CLAUDE.md files. The gap between this document and the issue reports below is the subject of the article.
The Pattern
1Plan-mode path conflict ↩
Issue #27032 is the clearest documented example of recency and specificity overriding the stated user-over-system hierarchy. Plan mode's built-in system prompt names a specific path (~/.claude/plans/...) where plan artifacts should be written. The user's CLAUDE.md forbids writing to that path, yet the model follows the system prompt because the plan-mode directive is both more specific (it names the exact path) and more recently injected into the context window. The maintainer thread acknowledges the conflict but frames it as a priority question rather than a bug, which is itself evidence that the user-facing contract needs revision.
anthropics/claude-code #27032.
2Co-Authored-By / attribution override ↩
Issue #17085 documents a long-running complaint: CLAUDE.md rules that forbid the Co-Authored-By: Claude commit footer are overridden by the system prompt's default instruction to add that footer. The model inserts the footer despite explicit user-level configuration to the contrary. This is a cleaner case than #27032 because there is no path-specificity argument: the user's rule is the more specific one, yet the system prompt still wins on recency. The thread includes multiple reproduction reports across months and model versions.
anthropics/claude-code #17085.
3CLAUDE.md overridden by system defaults ↩
Issue #21226 documents the same pattern as #17085 across a broader set of CLAUDE.md rules. System-level defaults take priority at runtime despite the documentation stating that user-level configuration should win. The issue is useful as corroboration that #17085 is not a one-off: multiple independent rule categories exhibit the same inversion, which argues against a per-rule bug and in favor of a structural precedence problem.
anthropics/claude-code #21226.
For Practitioners
4CLAUDE.md priority over skill instructions ↩
Issue #41437 extends the priority inversion pattern from the system prompt down to the skill layer. When both a skill and CLAUDE.md address the same subject, the skill's instructions win even though the documented hierarchy places user-level CLAUDE.md above skills. This matters for the practitioner advice in the article: checking for a conflicting skill is a concrete diagnostic step when a CLAUDE.md rule appears to be ignored, because skill instructions are loaded closer to the tool call and are typically more specific to the task at hand.
anthropics/claude-code #41437.