feat(init): scaffold managed .specify/.gitignore (#4000)

* feat(init): scaffold managed .specify/.gitignore

Write a manifest-tracked `.specify/.gitignore` during shared-infra install
so machine-local Spec Kit state stays out of version control while everything
else under `.specify/` remains shareable:

- `feature.json` — the current-feature pointer, rewritten on every feature
  switch (per-checkout state, not something to share).
- `extensions/*/local-config.yml` — per-machine extension config overrides.

The file is routed through the same overwrite/skip/preserve policy as shared
templates: `--force` refreshes it, user edits are preserved on re-init, and
uninstall removes it via the manifest. Addresses #2304.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: 98faefd1-9fc8-48fc-bd25-d4f3ccbb2ab9

* docs: correct .specify/.gitignore uninstall claim

The file is tracked in the shared-infra manifest (speckit.manifest.json),
not the per-integration manifest that `specify integration uninstall` loads.
Shared infrastructure is deliberately preserved on uninstall
(see test_uninstall_preserves_shared_infra), so `.specify/.gitignore` is
left in place rather than removed. Reword the code comment and core.md note
to state the actual behavior; keep the true benefits (force-refresh and
preserve-on-edit).

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: 98faefd1-9fc8-48fc-bd25-d4f3ccbb2ab9

* revert: drop manual CHANGELOG.md edit

CHANGELOG.md is auto-generated; do not hand-edit it.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: 98faefd1-9fc8-48fc-bd25-d4f3ccbb2ab9

* test: add .specify/.gitignore to integration file inventories

The complete-file-inventory tests assert an exact match of every file
produced by `specify init`. Now that shared infra scaffolds a managed
`.specify/.gitignore`, add it to the expected inventories so the exact-match
assertions pass on both sh and ps script types.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)

---------

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: 98faefd1-9fc8-48fc-bd25-d4f3ccbb2ab9

Author: mnriem

docs/reference/core.md

@@ -57,6 +57,8 @@ specify init my-project --integration copilot --preset compliance
 
 > **Two resolution axes.** `SPECIFY_INIT_DIR` selects the **project** (which directory contains `.specify/`); `SPECIFY_FEATURE_DIRECTORY` / `.specify/feature.json` select the **feature** within that project. They are independent — project first, then feature.
 
+> **Version control.** `specify init` scaffolds a managed `.specify/.gitignore` that excludes machine-local state — `feature.json` (the current-feature pointer, rewritten on every feature switch) and per-machine extension `extensions/*/local-config.yml` overrides — while leaving everything else under `.specify/` (constitution, templates, scripts, extension config) shareable so teams stay aligned. Like the rest of `.specify/`'s shared scripts and templates, the file is tracked in the shared-infrastructure manifest: your edits are preserved on re-init and `specify init --here --force` restores the managed content. It is intentionally left in place by `specify integration uninstall`, which only removes the uninstalled agent's own files.
+
 > **Symlinked project roots.** `SPECIFY_INIT_DIR` relocates *where* the project is, not *how* a command treats symlinks: each command keeps its existing cwd-path stance. Commands that traverse and write project files through broad input paths (`bundle`, `workflow run <file>`) refuse a symlinked `.specify/` to preserve write confinement. Other project-scoped commands keep their existing behavior when `SPECIFY_INIT_DIR` points at a project root, which may include following a symlinked `.specify/`.
 
 ## Check Installed Tools

src/specify_cli/shared_infra.py

@@ -16,6 +16,22 @@
 
 logger = logging.getLogger(__name__)
 
+# Managed ``.specify/.gitignore``. Keeps machine-local Spec Kit state out of
+# version control while leaving shareable project files (specs, constitution,
+# templates, scripts, extension config) tracked. Patterns are relative to the
+# ``.specify/`` directory the file lives in.
+SPECIFY_GITIGNORE_CONTENT = """\
+# Machine-local Spec Kit state — not meant to be shared.