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A free scan shows the junk files, broken settings and background clutter dragging Windows down - then fixes them in one click.Free scan · Windows 10 & 11When AGENTS.md instructions conflict, first identify which agent harness and session type is running: there is no universal precedence rule. Codex documents a specific hierarchy; GitHub Copilot CLI combines applicable instructions without defining a general winner; VS Code warns that discovery and merging vary by harness. Follow a documented rule for the tool you are using, and if none exists, reconcile the files or ask their owner to clarify.
Why the answer depends on the agent
AGENTS.md is not governed by one cross-tool standard. Codex, GitHub Copilot CLI, Copilot on GitHub, and VS Code can discover and combine instruction files differently. Even within VS Code, behavior can depend on whether the session uses the Local agent or an Agent Host harness. Before deciding which instruction wins, establish the exact tool and session type.
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For VS Code, nested AGENTS.md discovery by the Local agent is experimental and disabled by default unless enabled with chat.useNestedAgentsMdFiles. Agent Host sessions follow the selected harness’s rules. See VS Code’s custom-instructions documentation.
The Tool Desk
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| Tool or feature | Documented behavior | What to do when instructions conflict |
|---|---|---|
| Codex | Combines project instruction files from repository root down to the current working directory; closer project files override earlier project guidance when they conflict. Direct system, developer, or user prompt instructions take precedence over AGENTS.md. | Use Codex’s documented scope and ordering, while honoring higher-priority direct prompt instructions. |
| GitHub Copilot CLI | Combines applicable user-level and repository instruction files, but does not specify a general precedence order among them. | Do not infer a winner from file location or order. Resolve the contradiction in the instructions or ask their owner. |
| Copilot on GitHub | For Copilot working on GitHub, the nearest AGENTS.md takes precedence; repository-wide and matching path-specific instructions can also apply. | Apply this behavior only to that GitHub feature, not automatically to other Copilot sessions. |
| VS Code | Discovery and merge behavior can differ by session type and harness. VS Code advises against relying on file order or a universal precedence rule. | Confirm the active session type and selected harness; use that harness’s documented behavior. |
For Codex’s published precedence statements and current configuration details, consult OpenAI’s Introducing Codex and AGENTS.md configuration guide. For Copilot CLI and Copilot on GitHub, see the relevant CLI instructions documentation and GitHub repository-instructions documentation.
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Resolve the conflict step by step
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Identify the harness and session
Record whether you are using Codex CLI, GitHub Copilot CLI, Copilot on GitHub, or a VS Code Local or Agent Host session. Do not treat one product’s behavior as a rule for another.
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Check which files the harness can discover
Map the instructions that apply to the task: global or user-level files, repository-root files, nested files along the working path, and any path-specific instruction files. A file that exists but is not discovered cannot resolve the active session’s behavior.
In Codex, check the global Codex home and each project directory from repository root through the current working directory. Codex checks
AGENTS.override.mdbeforeAGENTS.mdat each directory, and may use configured fallback filenames. It stops at the current directory rather than searching deeper unrelated folders. The configuration guide specifies a default combined project-instructions limit of 32 KiB, so content beyond the configured limit may not be included.Recommended Free Tools
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*.instructions.mdfiles apply when theirapplyTopattern matches. Check the CLI documentation for the applicable locations and patterns. -
Apply only a documented precedence rule
In Codex, project instructions are concatenated from root to the current directory, and closer project guidance overrides earlier project guidance when they conflict. OpenAI’s published Codex system-message text also states that direct system, developer, or user instructions take precedence over AGENTS.md.
For Copilot CLI, the documentation says applicable instruction files are combined but does not establish a general precedence order. For VS Code, do not use file order as a substitute for a documented rule. Copilot on GitHub’s nearest-file behavior is specific to that feature.
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Remove ambiguity if no winner is defined
Edit the relevant instructions so they agree, or ask the person responsible for them which behavior is intended. If a rule should apply only to one area, scope it with a mechanism the selected harness supports, such as an applicable path-specific instruction file. VS Code recommends keeping user, repository, and organization requirements consistent.
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Verify discovery and behavior
Confirm which files were loaded, then test a representative task to see whether the intended rule is followed. For Codex, the documentation suggests asking it to report its instruction sources and auditing session logs when needed. In Copilot CLI, use
/instructionsto view discovered files and enable or disable individual ones. VS Code notes that confirming a file was discovered does not prove the agent followed it; a representative task checks that separately.
Codex details that can explain a surprising result
- One selected file per directory: At each project directory Codex includes at most one instruction file, preferring
AGENTS.override.md, thenAGENTS.md, then configured fallback filenames. In the global scope, a non-emptyAGENTS.override.mdreplacesAGENTS.md; only the first non-empty file is used at that level. - Instructions are assembled at startup: Codex builds its instruction chain when it starts; in a TUI this usually happens once per launched session. After changing the working directory or instructions, start a fresh run or session if the active set may be stale.
- Scope ends at the working directory: Codex does not search into deeper, unrelated directories. A more deeply nested file matters only when the task’s working path brings it into scope.
Keep the evidence and expectations in proportion
Official documentation explains how these tools discover and handle instructions, but it does not establish how frequently AGENTS.md conflicts occur or measure their effects. The practical answer is therefore tool-specific: inspect the active instruction set, apply only a documented precedence rule, and clarify conflicts the harness leaves unresolved.
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