agents-md-compiler

Compile ordered Markdown policy modules into one deterministic, verifiable AGENTS.md. The target can be global, repository-local, nested, or another explicit path. The runtime has no dependencies, performs no network access, invokes no shell, and uses no LLM.

The mental model

One manifest owns one ordered module set and one default target. The compiler does not need a scope flag because Codex scope comes from the target path and the startup working directory:

Purpose	Typical target	Verification context
Global policy	~/.codex/AGENTS.md	Isolated empty directory
Repository policy	<repo>/AGENTS.md	Repository root or descendant
Nested policy	<repo>/<area>/AGENTS.md	Target directory or descendant
Standalone export	Any new path	No Codex visibility promise

The same lock, validate, check, install, status, and rollback workflow applies to every target. verify-codex adds the startup directory needed to prove that Codex actually discovers project and nested targets.

Codex loads one global instruction file and then builds a project instruction chain from the project root toward its startup working directory. A closer file is applied later. See the official Codex AGENTS.md guide.

Why compile instruction files

Canonical modules are easier to review and reuse than one large hand-maintained file, but Codex needs a self-contained file at startup. This compiler connects those needs without hiding provenance:

• canonical Markdown modules remain the only editable policy sources;
• a strict manifest fixes the source set, order, and target;
• a portable lock records each lexical source path, byte size, and SHA-256;
• rendering preserves every accepted source byte between generated markers;
• checking detects source drift, output drift, a missing target, shadowing, and unmanaged content;
• installation is explicit, atomic, backed up, and concurrency-safe;
• rollback restores exact prior bytes and refuses after an external target edit;
• runtime verification inspects Codex prompt input instead of asking a model what it thinks it read.

The tool does not discover repositories, detect stacks, select targets, or generate multiple files from one manifest. It does not author, rewrite, summarize, lint-fix, normalize, or deduplicate policy prose.

Requirements and installation

• Python 3.14 or newer.
• Linux, macOS, or Windows.
• codex on PATH only for optional runtime visibility verification.

# Recommended: install as an isolated tool.
uv tool install agents-md-compiler

# Or run without installing.
uvx agents-md-compiler --help

# Or install into an existing environment.
pip install agents-md-compiler

Both invocation forms are equivalent:

agents-md-compiler --help
python -m agents_md_compiler --help

Global quickstart

init defaults to the active global base file and prints the exact lock command to run next.

# Creates policy/agents-md.toml and policy/modules/*.md.
agents-md-compiler init --directory ./policy --bundle-id personal-policy

# Create the target parent when this is a new Codex home.
mkdir -p ~/.codex

agents-md-compiler lock --manifest ./policy/agents-md.toml
agents-md-compiler validate --manifest ./policy/agents-md.toml
agents-md-compiler render --manifest ./policy/agents-md.toml --locked
agents-md-compiler check --manifest ./policy/agents-md.toml

# Preview writes nothing.
agents-md-compiler install --manifest ./policy/agents-md.toml

# Explicitly mutate the target.
agents-md-compiler install --manifest ./policy/agents-md.toml --apply

# Prove the active global file is visible without project instructions.
agents-md-compiler verify-codex --manifest ./policy/agents-md.toml

Repository quickstart

Run this from the repository root. The target argument resolves from the current directory. init serializes it relative to .agents, so the generated manifest contains the portable value ../AGENTS.md.

agents-md-compiler init \
  --directory ./.agents \
  --target ./AGENTS.md \
  --bundle-id project-policy

agents-md-compiler lock --manifest ./.agents/agents-md.toml
agents-md-compiler validate --manifest ./.agents/agents-md.toml
agents-md-compiler check --manifest ./.agents/agents-md.toml
agents-md-compiler install --manifest ./.agents/agents-md.toml
agents-md-compiler install --manifest ./.agents/agents-md.toml --apply

# Prove the repository file is visible from this startup directory.
agents-md-compiler verify-codex \
  --manifest ./.agents/agents-md.toml \
  --cwd .

For a nested target, use the same layout and pass a working directory equal to or below the target's parent:

agents-md-compiler verify-codex \
  --manifest ./.agents/backend/agents-md.toml \
  --cwd ./backend/service

CURRENT means the selected target is byte-identical to a fresh locked render. It does not claim that Codex discovers that target from every possible working directory. A successful verify-codex makes the visibility claim only for its reported startup directory.

Normal edit workflow

1. Edit canonical module files, never the generated target.
2. Review the module and manifest changes.
3. Run lock explicitly to refresh source identity.
4. Run validate and review render --locked when needed.
5. Run check to see whether the selected target needs installation.
6. Preview install, then rerun it with --apply.
7. Run verify-codex with the applicable startup context.

Editing a module after locking produces LOCK_STALE and exit code 2. Read-only commands never refresh a lock or install a target implicitly.

When --manifest is omitted, the CLI uses ./agents-md.toml. It falls back to legacy ./global-agents.toml only when the neutral default is absent. If both exist, the invocation is ambiguous and must use explicit --manifest.

Choosing a destination

• Manifest default_target is the persistent managed destination. A relative value resolves from the manifest directory. A leading ~ expands through the standard home lookup.
• --target PATH overrides the managed destination for one invocation. A relative command-line path resolves from the current working directory.
• render --locked --output PATH writes one standalone file only when the path does not exist. It never replaces an existing file or creates its parent.

Codex visibility is promised only for paths Codex actually discovers. A custom file name can still use compilation, checking, installation, and rollback, but a runtime probe will not pass unless Codex includes those bytes through its normal instruction discovery.

Adopting an existing AGENTS.md

An existing file without a recognized generated header is unmanaged and is never replaced silently. First preview the install and capture the current file digest. Then provide both adoption flags:

shasum -a 256 ./AGENTS.md

EXPECTED_TARGET_SHA256=<captured-64-character-digest>
agents-md-compiler install \
  --manifest ./.agents/agents-md.toml \
  --apply \
  --replace-unmanaged \
  --expect-target-sha256 "${EXPECTED_TARGET_SHA256}"

A digest mismatch refuses the write. A successful adoption stores the exact handwritten predecessor as a backup before replacing it.

Safety and operational state

All target mutations require --apply. Dry runs create no target, backup, receipt, deployment directory, or advisory lock.

New operational evidence is scoped by bundle ID and resolved target digest under the user state root:

• Linux and macOS: ${XDG_STATE_HOME:-~/.local/state}/agents-md-compiler/
• Windows: %LOCALAPPDATA%/agents-md-compiler/

Advisory locks live in one distribution-wide namespace and are keyed only by the resolved protected path. Two different bundle IDs therefore coordinate when they select the same target. Two targets using one bundle ID retain separate receipts, backups, preserved files, and last-install state.

Rollback consumes one explicit install receipt:

agents-md-compiler rollback \
  --manifest ./.agents/agents-md.toml \
  --receipt <path/to/install-receipt.json> \
  --apply

Rollback refuses unless the target still matches the receipt's installed digest. Backups are never deleted or rotated automatically. When an install created a previously missing target, rollback moves the generated file into private state instead of deleting it irrecoverably.

Other safety boundaries:

• sources and targets that are symbolic links are refused;
• target parents must already exist and be directories;
• a non-empty sibling AGENTS.override.md shadows a selected AGENTS.md and causes SHADOWED;
• a source may not alias the selected output;
• a source containing the compiler marker prefix is rejected;
• an unknown future rendered format is unmanaged and requires explicit adoption.

If a post-replacement step fails, recovery runs under the same target lock. It first proves that the target still contains the operation's bytes, then restores the predecessor from its verified backup or preserves a newly generated file and restores prior absence.

Format-1 migration

Current releases emit portable lock format 2 and neutral rendered format 2.

• A strict format-1 lock is migration input. Read-only commands report LOCK_STALE; explicit lock replaces it atomically with format 2.
• Exact format-1 and format-2 rendered targets are managed. A format-1 target is DRIFTED and upgrades through ordinary explicit install without unmanaged-file adoption flags.
• Upgrade installation backs up exact format-1 bytes. Receipt-based rollback can restore them when the format-2 target has not changed.
• Legacy bundle-only install receipts remain accepted for explicit validated rollback. New evidence is written only to target-qualified deployment state.

Repository CI

Commit the manifest, canonical modules, portable lock, and generated target when the repository chooses to track generated output. A read-only CI gate can run:

agents-md-compiler lock --manifest ./.agents/agents-md.toml --check
agents-md-compiler validate --manifest ./.agents/agents-md.toml
agents-md-compiler check --manifest ./.agents/agents-md.toml

verify-codex is an environment integration gate, not a deterministic unit gate. Run it where the intended Codex executable and startup context are available.

Determinism and preservation guarantees

• Equal manifest and source bytes produce equal format-2 lock and rendered bytes across checkout roots.
• Output contains no timestamp, host name, process ID, random value, temporary path, resolved source path, package version, or working directory.
• Manifest order is output order. Rendering does not enumerate source folders.
• Sources must be non-empty strict UTF-8 with LF line endings and exactly one final LF. BOM, NUL, CR, invalid UTF-8, and marker collisions are rejected.
• Accepted source bytes are copied exactly. The compiler never trims, reflows, normalizes, lint-fixes, summarizes, or deduplicates them.

Digests prove that bytes did not change between locking and rendering. They do not establish authorship, correctness, or safety. See docs/security-model.md.

JSON automation

Every command accepts --format json and emits exactly one JSON object to stdout. Diagnostics remain on stderr.

agents-md-compiler status \
  --manifest ./.agents/agents-md.toml \
  --format json

Drive automation from the exit code and inspect state for the reason:

Code	Meaning
0	Succeeded; CURRENT when a target state applies
1	Invalid invocation, input, I/O, or runtime verification failure
2	Read-only difference: LOCK_MISSING, LOCK_STALE, DRIFTED, MISSING
3	Safety refusal: SHADOWED, UNMANAGED_TARGET, CONCURRENT_CHANGE

--quiet suppresses non-error stderr. It never suppresses JSON or requested render output.

Codex verification limits

verify-codex resolves codex from PATH, captures codex --version, confirms that debug prompt-input is available, and searches the returned JSON for the generated marker, every module boundary, and unique content sentinels from the first and last modules.

For the active global base or override file, the probe runs from a disposable empty directory. For a project or nested target, it runs from explicit --cwd or the target parent. The project directory must be equal to or below the target parent.

The command sends no model request, requires no API authentication, changes no Codex configuration, and makes no semantic-compliance claim. Marker presence proves visibility, not obedience. If the debug interface is missing or changed, the state is RUNTIME_UNVERIFIED and the exact failing command is reported.

Documentation

Document	Contents
docs/manifest-v1.md	Manifest schema, path bases, and rejection rules
docs/rendered-format-v1.md	Frozen legacy lock and rendered format
docs/rendered-format-v2.md	Current portable lock and neutral rendered format
docs/cli-contract.md	Commands, options, JSON, states, and exits
docs/security-model.md	Trust, path, concurrency, and recovery boundaries
AGENTS.md	Generated project contract for repository agents
CONTRIBUTING.md	Development, tests, and release boundaries

License

MIT. See LICENSE.