Add e2e lifecycle coverage for existing installs

[markcallen]

Summary

• add standalone scripts/e2e-*.sh coverage for existing-install lifecycle and upgrade flows
• reconcile stale managed agent/skill artifacts and keep support-file sections in sync during wrapper refreshes
• extend doctor output to report taskSystem and update backend coverage for skill refresh and unreadable Claude archive recovery

Testing

• ./scripts/run-unit-tests-pre-push.sh except the final CLI go test step needed GOCACHE=/tmp/go-build-cli because the default cache path was read-only in this environment
• env GOCACHE=/tmp/go-build-cli go test ./... in cli/ballast
• go test ./... in packages/ballast-go
• uv run --python 3.12 python -m unittest tests.test_cli in packages/ballast-python
• pnpm --filter @everydaydevopsio/ballast run test -- doctor.test.ts
• for script in ./scripts/e2e-*.sh; do "$script"; done

Follow-up

• closes Audit smoke and e2e tests for naming, scope, best practices, and trigger policy #184

[codecov]

Codecov Report

❌ Patch coverage is 75.71885% with 76 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
cli/ballast/main.go	68.69%	48 Missing and 19 partials ⚠️
packages/ballast-typescript/src/install.ts	88.57%	8 Missing ⚠️
packages/ballast-typescript/src/doctor.ts	66.66%	1 Missing ⚠️

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[Copilot]

Pull request overview

This PR updates install patch behavior for Claude .skill archives so unreadable existing archives can be replaced with canonical packaged skill content instead of failing the install.

Changes:

• Adds Claude skill patch fallback logic in TypeScript and Python installers.
• Adds regression tests for unreadable Claude .skill archives in TypeScript and Python.
• Documents the recovery behavior in PRD.md.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
PRD.md	Adds the unreadable Claude .skill archive recovery requirement and acceptance criterion.
packages/ballast-typescript/src/install.ts	Introduces TypeScript fallback handling for Claude skill archive patching.
packages/ballast-typescript/src/install.test.ts	Adds TypeScript regression coverage for invalid Claude .skill archive replacement.
packages/ballast-python/ballast/cli.py	Adds Python fallback handling for Claude skill archive patching and changes common agent registration.
packages/ballast-python/tests/test_cli.py	Adds Python regression coverage for invalid Claude .skill archive replacement.

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[Copilot]

Pull request overview

Copilot reviewed 25 out of 25 changed files in this pull request and generated 5 comments.

[Copilot]

Pull request overview

Copilot reviewed 25 out of 25 changed files in this pull request and generated 6 comments.

[Copilot]

Pull request overview

Copilot reviewed 26 out of 26 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (3)

cli/ballast/main.go:2282

• For cursor/opencode, this condition allows deletion solely because the target matches, without checking that the stale skill was present in the previous .rulesrc.json or otherwise owned by Ballast. Since removeStaleManagedFiles builds candidates from every supported skill name, a user-authored .cursor/rules/<supported-skill>.mdc or .opencode/skills/<supported-skill>.md that was never managed by Ballast can be removed during refresh, violating the requirement to avoid deleting unrelated user files.

	for _, file := range stringDifference(allManagedSkillPaths(root, target), managedSkillPaths(root, target, next.Skills)) {
		if !ballastOwnsManagedFile(file) && !trackedPaths[file] && !allowConfigBackedStaleSkillRemoval(target, file) {
			continue

cli/ballast/main.go:2730

• Claude .skill archives generated by the backends currently contain the raw skill SKILL.md without the new Created by [Ballast] marker, so this ownership check returns false unless the path also appears in a managed support-file section. If a support file was disabled, skipped, deleted, or preserved as unmanaged, refresh reconciliation will leave stale Claude skill archives behind even though they were Ballast-installed.

	if strings.HasSuffix(path, ".skill") {
		reader, err := zip.NewReader(bytes.NewReader(content), int64(len(content)))
		if err != nil {
			return false
		}
		for _, file := range reader.File {
			if file.Name != "SKILL.md" {
				continue
			}
			rc, err := file.Open()
			if err != nil {
				return false
			}
			data, readErr := io.ReadAll(rc)
			_ = rc.Close()
			if readErr != nil {
				return false
			}
			return strings.Contains(string(data), ballastManagedMarker)

cli/ballast/main.go:2273

• Stale rule cleanup cannot remove cursor/opencode agent rules because those targets have no support-file tracking and generated agent rule files do not include the Created by [Ballast] marker used by ballastOwnsManagedFile. As a result, removing a saved agent and refreshing a cursor/opencode install leaves the old managed rule files in place instead of reconciling the retained target.

	for _, file := range stringDifference(allManagedRulePaths(root, target), managedRulePaths(root, target, next)) {
		if !ballastOwnsManagedFile(file) && !trackedPaths[file] {
			continue

[Copilot]

Pull request overview

Copilot reviewed 26 out of 26 changed files in this pull request and generated 4 comments.