fix: avoid paths-only feature context writes

[luohui1]

Description

Closes #3025 by preventing check-prerequisites --paths-only / -PathsOnly from rewriting .specify/feature.json when SPECIFY_FEATURE_DIRECTORY is only a temporary read-only override.

Both Bash and PowerShell paths now suppress feature context persistence only for paths-only mode; normal command execution continues to persist explicit feature directory context.

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv sync && uv run pytest
• Tested with a sample project (if applicable)

Additional validation run locally after splitting this PR:

• uv run --extra test pytest tests/test_check_prerequisites_paths_only.py -q - 4 passed, 5 skipped
• uvx ruff check tests/test_check_prerequisites_paths_only.py - passed
• git diff --check - passed

Manual test results

Agent: Codex (GPT-5) | OS/Shell: Windows 11 / PowerShell 7.5.4

Command tested	Notes
.specify/scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly	Covered by regression test for read-only .specify/feature.json behavior.

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (describe below)

This PR was implemented by Codex (GPT-5) acting as an AI coding agent on behalf of @luohui1. The agent read the repository contribution/security/code-of-conduct docs and issue templates, inspected the relevant code paths, implemented the changes, ran the validation listed above, and prepared this PR description.

[mnriem]

Please separate out in 3 PRs. Thanks!

[mnriem]

Thanks for this. The fix direction is right — --paths-only is documented as read-only path resolution, so it shouldn't write tracked files. A couple of requests before this lands:

1. Reframe the rationale. The PR/issue describes SPECIFY_FEATURE_DIRECTORY as "only a temporary read-only override," but that's not how it's defined in the code. In get_feature_paths() it's an explicit override that is deliberately persisted ("Persist to feature.json so future sessions without the env var still work"). Can you re-anchor the justification on the defensible claim — "--paths-only must not mutate tracked files" — rather than on the env var being temporary? Also worth a line confirming persistence is still covered by the non-paths-only commands (specify, setup-plan, setup-tasks, etc.), so the "future sessions still work" guarantee holds.

2. Drop the new SPECIFY_NO_PERSIST_FEATURE_JSON env var. It's a global back-channel for one bit of state, and the PowerShell path sets $env:SPECIFY_NO_PERSIST_FEATURE_JSON = '1' without ever unsetting it — so suppression leaks for the rest of the process and would silently disable persistence for any later in-process Save-FeatureJson call. Please pass this as a local parameter/switch instead:

• Bash: a flag/arg on get_feature_paths threaded down to _persist_feature_json.
• PowerShell: a [switch]$NoPersist on Get-FeaturePathsEnv passed to Save-FeatureJson.

That keeps it self-contained and removes the leak. (If there's a strong reason to keep the env var, the PS side at least needs to scope/unset it in a finally to match the inline scoping Bash already uses.)