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Update Codex environment config#52

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jscraik wants to merge 28 commits into
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feat/agent-mode
Open

Update Codex environment config#52
jscraik wants to merge 28 commits into
mainfrom
feat/agent-mode

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@jscraik jscraik commented May 10, 2026

Summary

  • Resolve merge conflicts in the stale feat/agent-mode branch against current main.
  • Keep the current mainline agent-mode implementation while preserving alias activation for --ai, --robot, and --auto.
  • Reject invalid risk-policy-gate --max-tier values instead of silently passing an unknown tier.
  • Add the TypeScript 6 deprecation guard required for the build path.

Checklist

  • Conflicts resolved against main.
  • Current CodeRabbit blockers addressed or made outdated by the conflict resolution.
  • Local validation completed.

Testing

  • npm ci
  • ./node_modules/.bin/tsc -p tsconfig.json --noEmit
  • ./node_modules/.bin/vitest run
  • npm audit --audit-level=moderate
  • npm run build
  • git diff --check && git diff --cached --check

Review artifacts

  • CodeRabbit thread: unknown --max-tier no longer silently passes.
  • CodeRabbit thread: agent aliases now participate in pre-parse activation.
  • CodeRabbit thread: stale review approval-count implementation was removed by resolving to current mainline command implementation.

Notes

  • This PR is still subject to GitHub/CodeRabbit checks after push.

jscraik and others added 26 commits April 7, 2026 02:46
Add --agent flag that enables AI-friendly command interpretation:

- Flexible entity ID parsing: q42, Q42, q-42 all normalized to Q42
- Intent recognition: 'wsearch get Q42' → 'entity get Q42'
- Detailed error messages with context, examples, and fix hints
- Flag aliases: --net → --network, --j → --json, etc.

New source files:
- src/agent.ts: Intent parsing, error help, fuzzy matching
- src/cli-errors.ts: Shared CliError class

Updated:
- src/cli.ts: Integrate agent mode in fail handlers
- src/types.ts: Add agent flag to CliGlobals
- README.md: Add agent mode section
- docs/AGENTS.md: Comprehensive agent integration guide

All 103 tests pass. Backward compatible.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Mark agent mode features as completed in implementation plan.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ort, function or class'

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
…ort, function or class'

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
…ort, function or class'

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Update project license to Apache License 2.0.

- Replace LICENSE file with Apache 2.0 text
- Update package.json license field
- Update README badge and license reference

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
P1: Preserve JSON error envelope when agent mode is enabled
- Check JSON mode first in emitUnhandledCliError
- Include agent help text within JSON error message when both --agent and --json are used
- Ensures consistent machine-parseable output for automation

P2: Gate relaxed entity-ID coercion behind --agent flag
- assertEntityId now only accepts flexible formats (q-42, q_42) when agent=true
- Strict validation (Q42 only) for normal mode
- Prevents silent conversion of malformed IDs in scripts

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
AGENTS.md:
- Fix shell example with comments after backslashes
- Add --user-agent to example commands that were missing it

agent.ts:
- Fix fixFlagOrder to handle flag-with-value pairs (e.g., --output file)

cli.ts:
- Add --agent to booleanOptions in isHelpLikeInvocation
- Add parseAgentIntent pre-parsing when --agent flag is detected
- Import normalizeEntityId and suggestCommand for agent preprocessing

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
AGENTS.md:
- Fix shell example: remove comments after backslashes
- Add --user-agent to examples that were missing it

README.md:
- Add --user-agent to all API command examples
- Change "All commands require" to "API commands require"

CLI_SPECIFICATION.md:
- Add --agent to global flags table
- Document flexible entity ID format in agent mode

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Update INTENT_PATTERNS regex to handle q-42, q_42 formats
- Update transform functions to normalize IDs (remove separators, uppercase)
- Fix search pattern to stop at first flag (avoid swallowing --json etc.)
- Update normalizeEntityId to handle optional separators
- Simplify fixFlagOrder to preserve caller intent (return [...args])

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add stub commands for harness CI pipeline:
- check-environment: Verify environment setup
- risk-policy-gate: Evaluate risk policy for files
- review-gate: Check PR review status
- evidence-verify: Verify evidence files
- remediate run: Run remediation tasks

These commands return success by default to allow the harness
pipeline to complete. They output JSON when --json flag is used.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Fixed 5 file(s) based on 9 unresolved review comments.

Co-authored-by: CodeRabbit <noreply@coderabbit.ai>
- Fix parseAgentIntent to skip option values when finding first command

- Fix resolveErrorContext to detect --json from raw argv (avoiding yargs defaults)

- Improve agent mode processing to handle option values correctly

- Always validate URL format in global check (catches invalid URLs in preview mode)

Fixes test failures:

- api-url validation now returns E_VALIDATION instead of E_POLICY

- JSON output with -o flag now creates parent directories correctly

- CLI args are properly preserved through intent parsing

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
P1: Relax SPARQL intent regex to allow --agent flag in argv

P1: Replace CommonJS require with ESM imports in attestation handler

P2: Add new harness commands to trailing-help allowlist

P2: Gate intent preprocessing on enabled --agent mode only

P2: Treat --agent=false as disabled in agent detection

P2: Accept hyphenated queries in search intent shorthand

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add --findings, --contract, and --mode options to remediate run command

for Harness CI compatibility.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add typecheck, lint, and check scripts as aliases to existing scripts.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Remove unused fixFlagOrder function (dead code)

- Fix fail handler to include agent-formatted error in JSON output

  for consistency with emitUnhandledCliError

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Fix shell snippet in AGENTS.md (move comments before command)

- Fix rate limiting example to include --user-agent

- Remove exit code 4 from spec (not implemented)

- Fix normalizeEntityId regex to match assertEntityId flexibility

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Why: generated prek hooks default to ~/.cache/prek, which can fail in sandboxed environments.\n\nWhat: patch installed prek shim scripts with a repo-local PREK_HOME export after prek install and route Makefile hooks through the setup script.\n\nImpact: git hook execution no longer depends on writable home-directory cache paths.

Co-authored-by: Codex <noreply@openai.com>
Co-authored-by: Codex <noreply@openai.com>
Co-authored-by: Codex <noreply@openai.com>
Why: project-local governance defaults and environment/tooling checks needed to be executable inside this repo without relying on workspace-level scripts.

What: add local hook-governance scripts with explicit required inputs, add verify-work wrapper with explicit workspace mode, add repo scope artifacts/docs, and wire minimal mise + check-environment canonical tooling generation.

Impact/Risk: governance checks now default local and workspace checks are opt-in; low runtime risk, but docs and scripts changed across the repo.

Co-authored-by: Codex <noreply@openai.com>
Refresh the repo-local Codex environment file from the canonical harness template so setup and action commands stay aligned with current project scripts.

Co-authored-by: Codex <noreply@openai.com>
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Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: 9837a26d-128e-4960-b596-89326ae3d966

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Reviewing files that changed from the base of the PR and between 679561d and a8ab6e4.

📒 Files selected for processing (3)
  • src/agent.ts
  • src/cli.ts
  • tsconfig.json
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  • Create PR with unit tests
  • Commit unit tests in branch feat/agent-mode
  • 🛠️ harness docs parity: Commit on current branch
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💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 0d49f7851e

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

  • Open a pull request for review
  • Mark a draft as ready
  • Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

Comment thread src/cli.ts Outdated
Comment on lines +1718 to +1722
const maxTierIndex = tierOrder.indexOf(maxTier);

for (const [tierName, tierConfig] of Object.entries(contract.tiers || {})) {
const tierIndex = tierOrder.indexOf(tierName);
if (tierIndex > maxTierIndex) continue; // Skip tiers above max allowed
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P1 Badge Reject unknown max-tier values before evaluating policy

The gate never validates --max-tier, so an unrecognized value (for example --max-tier med) yields maxTierIndex === -1 and causes every configured tier to be skipped by if (tierIndex > maxTierIndex) continue, letting all file changes pass policy checks. This creates a silent policy bypass on typos or misconfigured automation and should fail fast with a usage/validation error when the tier is not one of low|medium|high|critical.

Useful? React with 👍 / 👎.

Comment thread src/cli.ts Outdated
Comment on lines +1837 to +1839
const reviews = await reviewsResponse.json() as Array<{ state?: string }>;
const approvals = reviews.filter((r: { state?: string }) => r.state === "APPROVED").length;
const minApprovals = contract.minApprovals || 1;
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P1 Badge Count approvals per reviewer, not per review event

This counts every APPROVED review event, but GitHub review history can contain multiple approvals from the same reviewer, so a single person re-approving can satisfy minApprovals incorrectly. In repos that require distinct approvers, this can produce false passes for review-gate; approvals should be computed from each reviewer’s latest state (or unique approved reviewers), not raw event count.

Useful? React with 👍 / 👎.

Comment thread src/cli.ts
Comment on lines +740 to +742
const isAgentMode = isAgentEnabled(rawArgv);
if (isAgentMode) {
// Only run intent parsing when agent mode is explicitly enabled
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P2 Badge Enable agent aliases during pre-parse activation

Agent pre-processing is gated by isAgentEnabled(rawArgv), but that helper only recognizes --agent forms. As a result, aliases declared in src/agent.ts (like --ai, --robot, --auto) never activate agent parsing/normalization and are treated as unknown flags in strict mode. If these aliases are intended to work, activation must also recognize them before the pre-parse gate.

Useful? React with 👍 / 👎.

jscraik and others added 2 commits May 10, 2026 15:13
Co-authored-by: Codex <noreply@openai.com>
Co-authored-by: Codex <noreply@openai.com>
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Codex usage limits have been reached for code reviews. Please check with the admins of this repo to increase the limits by adding credits.

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💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 684ddc8abe

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

  • Open a pull request for review
  • Mark a draft as ready
  • Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

Comment thread src/cli.ts
Comment on lines +731 to +733
if (value === "true") return true;
if (value === "false") return false;
// Don't treat other --flag=* forms as enabled (must be explicit true)
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P2 Badge Normalize aliased agent flags with explicit boolean values

isAgentEnabled now treats --ai=true/--robot=true as enabling agent mode (and =false as disabling), but the preprocessing path only rewrites exact alias tokens like --ai to --agent. That leaves --ai=true (or --ai=false when preprocessing is skipped) in processedArgv, and .strict() later rejects it as an unknown option, so explicit boolean alias forms still fail despite being recognized here. Normalize --ai|--robot|--auto=<value> to --agent=<value> before yargs parsing.

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