update-deps

name	update-deps
description	Audit and fix dependency vulnerabilities in Go and Node.js packages. Runs govulncheck for Go and npm audit for each package.json directory. Commits fixes directory by directory.
argument-hint	--fix

Audit and fix dependency vulnerabilities in this project. Follow the steps below in order.

Step 1: Go Vulnerability Check

Run govulncheck in every Go module in the repository:

make govulncheck
cd custombuild && make govulncheck
cd e2e && make govulncheck
cd k6 && make govulncheck
cd packagetracker && make govulncheck

Use the module's own make govulncheck target if it exists; otherwise run go tool govulncheck ./... from that module root.

Parse the output:

• If there are no vulnerabilities, note it and move on.
• If there are vulnerabilities, for each affected module:
  1. Run go list -m -u <module> to find the latest available version.
  2. Compare the current version with the latest version:
  • If the major version changes (e.g. v1.x.x → v2.x.x), this is a major version upgrade. Generate a Breaking Change Report for it (see below), defer the upgrade, and continue with any other patchable work.
  • If only minor/patch version changes, proceed automatically.
  3. After all patchable fixes are applied and any deferred major upgrades have been presented to the user for a decision, run go get <module>@latest then go mod tidy in all relevant directories:
     • ./
     • ./custombuild
     • ./e2e
     • ./k6
     • ./packagetracker

Important:

• go get <module>@latest is for Go module dependencies only. Do not use it to change the Go toolchain version.
• If the requested fix is a Go version bump, update the repository's Go version files and generated inputs directly instead of trying to solve it with go get:
  • flake.nix
  • .tool-versions
  • go.mod
  • custombuild/go.mod
  • e2e/go.mod
  • k6/go.mod
  • packagetracker/go.mod.tpl
  • custombuild/cmd/authgearx/Dockerfile
  • custombuild/cmd/portalx/Dockerfile
  • cmd/portal/Dockerfile
  • cmd/authgear/Dockerfile
  • once/partial.dockerfile
  • regenerate once/Dockerfile with make once/Dockerfile
  • run make go-mod-tidy
• If a Go version bump is needed, verify the repository-specific generation and build steps after editing the version files. Do not commit a toolchain bump that only changes go.mod without updating the other affected files.

Breaking Change Report for Go (major version bumps) must include:

• Module name, current version → proposed version
• Link to the module's changelog or migration guide if available (check the module's repository)
• Known incompatibilities (import path changes, removed/renamed symbols)
• Note that the upgrade is deferred until the end of the patchable-fix pass, then ask: "Do you want to apply this major version upgrade? (yes/no)"

After updating Go deps:

• Run make build or go build ./... to verify the build.
• If the build breaks, report the compiler errors and ask the user how to proceed. Do not commit.
• If vulnerabilities cannot be fixed (no fix available), note them in an Unfixable Issues Report and notify the user.
• If fixes were applied and build passes, stage and commit all affected Go module files, including go.sum, go.mod, custombuild/go.sum, custombuild/go.mod, e2e/go.sum, e2e/go.mod, k6/go.sum, k6/go.mod, and packagetracker/go.sum/packagetracker/go.mod when they change, with commit message: chore: fix Go dependency vulnerabilities

Step 2: Node.js Audit — directory by directory

Process each directory that contains a package.json (excluding node_modules) in this order:

1. portal/
2. authui/
3. portalgraphiql/
4. scripts/npm/

For each directory:

1. cd into it and check for stale overrides in package.json before auditing. For each entry in the "overrides" field:

   • Identify what vulnerability or issue the override was originally added to fix (check git log: git log --oneline -10 -- <dir>/package.json).
   • Run npm list <overridden-package> --all to see the currently resolved versions.
   • Check if the parent package that originally required the vulnerable version has since released a patch that bundles a safe version on its own (i.e. the override is no longer needed to satisfy the advisory).
   • If the override is no longer needed, remove it only after you have evidence that the vulnerable resolved versions are gone. Then run npm install and confirm with npm audit that there are no regressions before proceeding. Include the removal in the same commit as any other fixes for this directory.
   • Do not remove an override speculatively just to "see what happens". If removing it causes npm audit to re-report the vulnerability, restore the override and treat it as still required.
   • If npm list shows a vulnerable transitive version that is still being suppressed by an override, keep the override unless you can point to a non-vulnerable resolved version or an upstream package release that makes the override redundant.

   After removing any override and running npm install, you MUST verify the removal was safe:

   • Run npm ci --dry-run — if it fails, the removal broke the lockfile. Restore the override.
   • Run npm ls <overridden-package> --all 2>&1 | grep -E "UNMET|invalid" — any UNMET result means a package now depends on a version that isn't available. Restore the override.
   • Check every package that previously used the removed override still has a compatible resolved version. Inspect node_modules/<parent-pkg>/package.json for its declared dep range on the overridden package, and confirm the now-resolved version satisfies that range. If the resolved version is a different major, the removal is incorrect — restore the override or add a scoped replacement.

   The same verification applies when npm install shrinks the lockfile in any other way (e.g. deduplication removes nested entries). Treat any reduction in nested node_modules/.../node_modules/ entries as an implicit override removal and apply the same checks above before committing.

2. Run npm audit --json.

3. Parse the output:

   • If no vulnerabilities, note it and move on to the next directory.
   • Before applying any fix, inspect what versions npm audit fix would install by running npm audit fix --dry-run --json. For each package that would be updated:
     • If the proposed fix is a major version bump (semver major increases), it is a potential breaking change regardless of whether the build will pass.
     • Collect all such packages into a Breaking Change Report listing:
       • Package name, current version → proposed version
       • Semver change type (major bump)
       • Any notes from the advisory about incompatible changes
     • Do not apply the major upgrade automatically. Defer it, continue with any patchable fixes in other packages/directories, and report it in the final summary for a user decision.
   • For fixes with only minor/patch version bumps, run npm audit fix automatically.
   • If the user later confirms the breaking changes, run npm audit fix --force (only after confirmation), then verify build and commit that directory.
   • If a vulnerability can only be fixed by a major version bump, do not apply it automatically. Record it in the Breaking Change Report and revisit it only after all patchable fixes have been applied.
   • If vulnerabilities are unfixable via npm audit fix (i.e. npm audit fix --dry-run shows no resolution), check if the vulnerability is in a transitive dependency whose parent has not yet released a patch:
     1. Identify the vulnerable transitive package and the minimum safe version that fixes it (from the advisory).
     2. Run npm list <transitive-package> --all to see every installed version of that package across the dependency tree. This is critical — there may be multiple versions installed at different semver ranges (e.g. 3.x, 9.x, 10.x). Only the version(s) that fall in the advisory's vulnerable range need to be overridden. Record this full list — it is your baseline.
     3. Identify the direct parent package(s) that pull in the vulnerable version (e.g. eslint-plugin-sonarjs → minimatch@10.1.2).
     4. Check the changelog/release notes between the currently-used vulnerable version and the safe version:
        • Look for any breaking changes (API removals, changed behavior, new peer-dep requirements).
        • If there are no breaking changes, add a scoped override to package.json, targeting only the parent package that pulls in the vulnerable dep. Do NOT use a flat global override — it will forcibly replace all other installed versions (including non-vulnerable ones) and break unrelated packages:

          "overrides": {
            "<direct-parent-package>": {
              "<transitive-package>": "^<safe-version>"
            }
          }
          

          Then run npm install to apply. Before accepting the result, run npm list <transitive-package> --all again and diff it against your baseline: only the targeted parent's instance should have changed version. If any other package's resolved version of <transitive-package> changed, the override is broader than intended — remove it and use a more specific scope or a per-parent override. Then run npm audit to confirm the vulnerability is resolved.
        • If there are breaking changes, do not apply the override. Add the vulnerability to the Unfixable Issues Report and explain why the override is unsafe.

4. After any npm operation that changes the lockfile, run these two validation checks before touching the build or committing:

   a) Lockfile self-consistency Run npm ci --dry-run. If it fails with "Missing: @ from lock file", the lockfile is inconsistent and must be fixed before proceeding. Do not commit a lockfile that fails npm ci.

   b) Silent dedup detection If the lockfile shrank significantly (many deletions, few or no insertions), nested package entries may have been removed by npm's deduplication. Removed nested entries are usually fine — unless a package's declared dependency range is no longer satisfied by the hoisted version.

   Run: git diff -- package-lock.json | grep "^-" | grep '"node_modules/.*/node_modules/' | grep -o '"[^"]*node_modules/[^"]*"' | sort -u

   For each removed nested path (e.g. node_modules/@eslint/config-array/node_modules/minimatch), extract the parent package and transitive package name. Then check:

   npm ls <transitive-package> 2>&1 | grep -E "UNMET|invalid|extraneous"
   

   Also inspect the parent's own package.json on disk (node_modules/<parent>/package.json) to find its declared range for the transitive dep. If the hoisted version does NOT satisfy that range (different major), the dedup is silent but incorrect.

   Fix: Add a scoped override in the directory's package.json to make the upgrade intentional:

   "overrides": {
     "<parent-package>": {
       "<transitive-package>": "^<hoisted-safe-version>"
     }
   }
   

   Then run npm install and re-run npm ci --dry-run to confirm.

   c) Jest peer alignment (authui only) After any npm operation in authui/, run:

   npm ls jest-environment-jsdom jest-runtime 2>&1 | grep -E "jest-environment-jsdom|jest-runtime"
   

   Both must resolve to the same major.minor. If jest-runtime is at 30.4.x but jest-environment-jsdom is still pinned to ^30.2.0 in package.json, update the pin to ^30.4.0 (matching the runtime minor), then run npm install. Misalignment causes a runtime error (clearMocksOnScope is not a function) that only surfaces when tests run — not during install.

5. After applying fixes in a directory, verify the project still builds:

   • For portal/: npm run build (or npm run typecheck if faster)
   • For authui/: npm run build
   • For portalgraphiql/: npm run build
   • For scripts/npm/: skip build check (utility scripts)

6. Stage and commit changes for that directory immediately:

   • git add <dir>/package.json <dir>/package-lock.json
   • If overrides were added, include a comment in the commit body explaining which transitive dep was pinned, why, and a link to the advisory.
   • Commit message: chore: fix npm dependency vulnerabilities in <dir>

Step 3: Final Summary

After all directories are processed, output a summary with three sections:

Fixed

List every package that was updated (name, old version → new version, directory).

Breaking Changes Applied

List any breaking changes that were confirmed and applied.

Unfixable Issues

List any vulnerabilities that could not be resolved, including:

• Package name and version
• CVE/advisory ID
• Why it cannot be fixed — be specific:
  • No patch released yet by the package author
  • Transitive dependency where the override would introduce breaking changes (explain what breaks)
  • Locked by another dependency with no compatible version
• Recommended action (e.g., open issue with upstream, watch for future patch, manual code workaround)