If Claude Code seems to ignore project guidance, first check what it actually loaded: run /context and review the Memory files list. Then trace the applicable instruction files and imports, check whether AGENTS.md is enabled, and reconcile contradictory rules in their source files. File order affects what enters context, but it does not reliably decide which conflicting instruction Claude follows.
1. Check which instruction files Claude Code loaded
In the affected session, run /context and inspect the Memory files list. Record the paths shown and confirm the session started from the expected working directory. If a file is absent, Claude Code cannot follow it as loaded project memory; investigate discovery conditions and project-instruction settings before rewriting that file.
Loading depends on where Claude Code is working. Applicable CLAUDE.md and CLAUDE.local.md files in ancestor directories load at startup. Instruction files in a nested directory are loaded when Claude works in that subtree. A file in a sibling directory may therefore be irrelevant to the current task. See Anthropic’s Claude Code Memory documentation for the current discovery behavior.
2. Trace all applicable instructions and imports
Start at the working directory, then check its parent directories up to the filesystem root. Inspect relevant nested directories as well as project and user rules. Follow every @path import in a loaded file, including imports within imported files.
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CLAUDE.mdandCLAUDE.local.mdfiles in the working directory and its ancestors- Nested instruction files under the subtree Claude is editing
- Project rules in
.claude/rules/and personal rules in~/.claude/rules/ - Every referenced
@pathfile and any further imports it contains
Relative import paths resolve from the file containing the import, not from the shell’s current directory. Imports are expanded at startup, can recurse up to four hops, and may prompt for approval when they point outside the project. Import syntax in code spans and fenced code blocks is not parsed as an import. Imports organize instructions but do not reduce their context use.
For each instruction, note its exact path, the behavior it governs, whether it is still current, and whether another file gives an incompatible direction. Keep team-shared project requirements separate from personal preferences so changes go into the right file.
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3. Diagnose why Claude Code may not read AGENTS.md
AGENTS.md has conditional loading behavior. In the default setup, Claude Code reads it when no CLAUDE.md, .claude/CLAUDE.md, or CLAUDE.local.md exists in the working directory or an ancestor. If one of those Claude files is present, AGENTS.md is not read by default.
To include both, open /config and set Project instructions to claude-md-and-agents-md, or import AGENTS.md from CLAUDE.md. Check claude --version as well: the documentation lists v2.1.277 as the minimum for direct AGENTS.md support and describes session cases where that support may be unavailable before v2.1.281. Importing from CLAUDE.md is the documented fallback when direct loading is unavailable. Confirm Project instructions is not set to claude-md or managed-only if you expect AGENTS.md to load.
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4. Resolve the actual contradiction
Compare the instructions’ meaning, not just filenames, timestamps, or which file appears last. Ancestor files are ordered from filesystem root toward the working directory; in the same directory, CLAUDE.local.md is appended after CLAUDE.md. User rules load before project rules. Those ordering details describe context assembly, not a dependable override system.
Anthropic warns: “If two instructions conflict, Claude may follow either one arbitrarily.” Remove stale guidance, combine compatible rules, and make the remaining directions specific. Do not rely on a later file or a higher position in the loaded context to win.
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In a monorepo, also inspect claudeMdExcludes, which can exclude matching CLAUDE.md or rule paths. Managed policy CLAUDE.md files cannot be excluded. Anthropic distinguishes technically enforced managed settings from behavioral guidance written in CLAUDE.md; use the appropriate mechanism for the requirement.
5. Use the prompt audit when available
With Claude Code v2.1.283 or later, run /doctor prompt-audit. It checks for outdated model instructions, references to nonexistent files or commands, and contradictions. The default scope includes CLAUDE.md, CLAUDE.local.md, AGENTS.md, rules, skills, commands, subagents, and output styles under .claude/ and ~/.claude/. You can specify a file or directory to narrow the audit.
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The audit reports issues and proposes edits; it does not change files until you request those edits. Review proposed changes against your intended project behavior before accepting them.
6. Keep the repaired instruction set manageable
- Keep each
CLAUDE.mdunder Anthropic’s recommended target of 200 lines; longer files consume more context and may reduce adherence. - Files over 4 MiB are skipped.
- Use path-scoped rules for guidance needed only when Claude handles matching files.
- Review nested and imported instructions alongside the top-level file when guidance changes.
Splitting a long instruction set into imported files can make it easier to organize, but it does not lower the total context cost.
Quick Recap
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