Unify workflow scripts under a single Python implementation per command

[mnriem]

Goal

Replace the paired bash (.sh) + PowerShell (.ps1) scripts with one Python script per occurrence, eliminating dual-maintenance and the jq/manual-JSON divergence. The specify CLI is already Python, so the interpreter is guaranteed present — no new runtime dependency.

Scope

~4,500 lines across ~10 script pairs:

• Core scripts/{bash,powershell}/ — common, check-prerequisites, create-new-feature, setup-plan, setup-tasks
• extensions/agent-context/scripts/ — update-agent-context
• extensions/git/scripts/ — git-common, initialize-repo, auto-commit, create-new-feature-branch

Strategy

Incremental. Introduce py as a third script type alongside sh/ps, port one script end-to-end as a proof of concept with output-parity tests, then migrate the rest. Only after parity is proven do we consider deprecating sh/ps.

Contract to preserve

Agents parse script stdout (FEATURE_DIR:…, AVAILABLE_DOCS:…, JSON shapes, and the --json / --paths-only / --require-tasks / --include-tasks flags). Behavioral parity is the acceptance bar for every port.

Sub-issues

• Add py script type & interpreter resolution #3278 — Add py script type & interpreter resolution (foundation)
• PoC: port check-prerequisites to Python with output-parity tests #3279 — PoC: port check-prerequisites to Python + parity tests (depends on Add py script type & interpreter resolution #3278)
• Port core scripts to Python (common, create-new-feature, setup-plan, setup-tasks) #3280 — Port core common + create-new-feature + setup-plan + setup-tasks (depends on PoC: port check-prerequisites to Python with output-parity tests #3279)
• Port agent-context extension scripts to Python #3281 — Port agent-context extension scripts (depends on PoC: port check-prerequisites to Python with output-parity tests #3279)
• Port git extension scripts to Python #3282 — Port git extension scripts (depends on PoC: port check-prerequisites to Python with output-parity tests #3279)
• Add py: lines to command templates' scripts: frontmatter #3283 — Update templates' scripts: frontmatter to add py: lines (depends on Port core scripts to Python (common, create-new-feature, setup-plan, setup-tasks) #3280–Port git extension scripts to Python #3282)
• Docs and migration/deprecation plan for Python scripts #3284 — Docs, AGENTS.md, and migration/deprecation plan (depends on Add py: lines to command templates' scripts: frontmatter #3283)

Out of scope (for now)

Removing .sh/.ps1 files. They stay until py reaches full parity and adoption.