e2e: cover init phase and lint negative and overwrite paths

[codeaholicguy]

Current coverage

Happy paths for init, adding one phase, and parseable lint JSON exist; non-interactive safety, reruns, overwrite behavior, and precise lint contracts remain partial or absent.

What is missing

• init --yes required selection validation
• Rerun preservation without overwrite and replacement with --overwrite
• Invalid YAML/JSON templates, duplicate/invalid phases, path conflicts, and user-edited files
• phase with no name, invalid/duplicate phase, custom docs path, and uninitialized project
• Known passing/failing lint workspaces, exact check IDs/counts, exit codes, feature docs, worktree diagnostics, and invalid feature names
• Complete top-level/subcommand help exposure

Risk ranking

Low-to-medium, rank 14: core happy paths exist, but gaps can allow destructive or misleading workflow behavior.

Recommended E2E tests

• Cover init --yes, missing required selections, repeat without overwrite, repeat with overwrite, invalid template, and exact preservation of user-edited files.
• Construct one known failing and one passing workspace and assert lint check IDs, summary counts, feature diagnostics, and exit codes.

Acceptance criteria

• The checklist tests are merged under e2e/.
• Phase negative/idempotent cases and complete help discovery are included.
• Tests prove user-edited files survive unless overwrite is explicit.

Related audit findings

No direct A/C defect; issue #77 and D1 are related to init/docs behavior in multi-repository workspaces.