chore: add .pre-commit-config.yaml and fix trailing whitespace

[vincentclee]

Adds a .pre-commit-config.yaml with trailing-whitespace, end-of-file-fixer, check-yaml, and check-executables-have-shebangs hooks (excluding .lock.yml files generated by gh-aw).

Fixes 41 files with trailing whitespace or missing end-of-file newlines, including shipped templates (tasks.md, plan.md, specify.md, etc.) that cause managed-files-modified warnings in user projects when their own pre-commit hooks clean up these issues after specify init.

Changes

• New: .pre-commit-config.yaml — prevents future trailing whitespace/newline regressions
• Fixed: 41 files with trailing whitespace or missing EOF newlines (templates, scripts, tests, config files)

Why

Users with pre-commit hooks (trailing-whitespace, end-of-file-fixer) get specify integration status warnings about modified managed files because the shipped templates contain trailing whitespace that pre-commit correctly strips, causing checksum mismatches.

[Copilot]

Pull request overview

Adds a repo-level pre-commit configuration to prevent trailing whitespace / missing EOF newline regressions, and normalizes existing files (including shipped templates) to avoid user-facing “managed-files-modified” warnings when users run their own formatting hooks after specify init.

Changes:

• Added .pre-commit-config.yaml with basic hygiene hooks (trailing-whitespace, end-of-file-fixer, check-yaml, check-executables-have-shebangs) and exclusions for generated *.lock.yml.
• Normalized trailing whitespace / EOF newlines across templates, scripts, tests, and misc repo files.
• Minor whitespace-only cleanup in integration/test/docs content.

Show a summary per file

File	Description
.pre-commit-config.yaml	Adds pre-commit hooks to prevent whitespace/EOF regressions (excludes *.lock.yml).
tests/test_timestamp_branches.py	Removes trailing whitespace at EOF.
tests/test_setup_tasks.py	Removes trailing whitespace on blank lines throughout the test file.
tests/test_merge.py	Removes trailing whitespace on blank lines in tests.
tests/test_extension_update_hardening.py	Removes trailing whitespace on blank lines in tests.
tests/test_extension_registration.py	Removes trailing whitespace on blank lines in tests.
tests/integrations/test_integration_vibe.py	Ensures file ends with newline / removes EOF formatting noise.
tests/integrations/test_integration_forge.py	Removes trailing whitespace on blank lines in tests.
tests/integrations/test_integration_devin.py	Ensures file ends with newline / removes EOF formatting noise.
tests/integrations/test_integration_cursor_agent.py	Removes trailing whitespace at EOF.
tests/hooks/TESTING.md	Removes trailing whitespace in documentation.
tests/hooks/.specify/extensions.yml	Removes trailing whitespace in YAML fixture.
templates/vscode-settings.json	Removes trailing whitespace / ensures proper EOF newline.
templates/commands/tasks.md	Removes trailing whitespace in shipped command template frontmatter/body.
templates/commands/specify.md	Removes trailing whitespace in shipped command template frontmatter/body.
templates/commands/plan.md	Removes trailing whitespace in shipped command template frontmatter.
templates/commands/implement.md	Removes trailing whitespace in shipped command template body.
templates/commands/constitution.md	Removes trailing whitespace in shipped command template frontmatter.
templates/commands/clarify.md	Removes trailing whitespace in shipped command template frontmatter.
templates/checklist-template.md	Removes trailing whitespace in shipped template comments.
src/specify_cli/integrations/forge/__init__.py	Removes trailing whitespace in docstring/comments.
src/specify_cli/integrations/devin/__init__.py	Ensures proper EOF newline.
spec-kit.code-workspace	Ensures proper EOF newline.
scripts/powershell/setup-plan.ps1	Removes trailing whitespace in hashtable/object literal formatting.
scripts/powershell/common.ps1	Removes trailing whitespace on blank line.
scripts/powershell/check-prerequisites.ps1	Removes trailing whitespace and normalizes spacing in output blocks.
scripts/bash/setup-plan.sh	Removes trailing whitespace and ensures proper EOF newline.
scripts/bash/create-new-feature.sh	Removes trailing whitespace on blank lines.
scripts/bash/check-prerequisites.sh	Removes trailing whitespace on help/output spacing.
pyproject.toml	Removes trailing whitespace at EOF.
newsletters/2026-March.md	Removes trailing blank lines at EOF.
LICENSE	Removes trailing whitespace at EOF.
extensions/selftest/commands/selftest.md	Removes trailing whitespace in documentation.
extensions/catalog.json	Ensures proper EOF newline.
docs/.gitignore	Removes trailing whitespace at EOF.
.markdownlint-cli2.jsonc	Ensures proper EOF newline.
.github/workflows/stale.yml	Removes trailing whitespace in workflow YAML.
.github/PULL_REQUEST_TEMPLATE.md	Removes trailing whitespace at EOF.
.github/ISSUE_TEMPLATE/preset_submission.yml	Removes trailing whitespace in YAML template.
.github/ISSUE_TEMPLATE/extension_submission.yml	Removes trailing whitespace in YAML template.
.github/ISSUE_TEMPLATE/agent_request.yml	Removes trailing whitespace in YAML template.
.github/CODEOWNERS	Removes trailing whitespace at EOF.

Review details

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• Files reviewed: 11/42 changed files
• Comments generated: 0
• Review effort level: Low

[mnriem]

Thank you!