fix: stop check-prerequisites --paths-only from writing feature.json (#3025)

scripts/bash/check-prerequisites.sh

@@ -78,8 +78,14 @@ done
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
-# Get feature paths
-_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+# Get feature paths.
+# In --paths-only mode this is pure resolution, so pass --no-persist to opt out
+# of the feature.json write side effect (issue #3025).
+if $PATHS_ONLY; then
+    _paths_output=$(get_feature_paths --no-persist) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+else
+    _paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+fi
 eval "$_paths_output"
 unset _paths_output
 

scripts/bash/common.sh

@@ -152,6 +152,15 @@ _persist_feature_json() {
 }
 
 get_feature_paths() {
+    # Read-only callers (e.g. check-prerequisites.sh --paths-only) pass
+    # --no-persist so pure path resolution never writes .specify/feature.json,
+    # which would dirty the working tree or overwrite a pinned value (issue #3025).
+    local no_persist=false
+    if [[ "${1:-}" == "--no-persist" ]]; then
+        no_persist=true
+        shift
+    fi
+
     # Split decl/assignment so a SPECIFY_INIT_DIR validation failure in
     # get_repo_root propagates as a hard error instead of being masked by `local`.
     local repo_root
@@ -168,8 +177,11 @@ get_feature_paths() {
         feature_dir="$SPECIFY_FEATURE_DIRECTORY"
         # Normalize relative paths to absolute under repo root
         [[ "$feature_dir" != /* ]] && feature_dir="$repo_root/$feature_dir"
-        # Persist to feature.json so future sessions without the env var still work
-        _persist_feature_json "$repo_root" "$SPECIFY_FEATURE_DIRECTORY"
+        # Persist to feature.json so future sessions without the env var still
+        # work — unless the caller opted out for read-only resolution (#3025).
+        if [[ "$no_persist" != true ]]; then
+            _persist_feature_json "$repo_root" "$SPECIFY_FEATURE_DIRECTORY"
+        fi
     elif [[ -f "$repo_root/.specify/feature.json" ]]; then
         local _fd
         _fd=$(read_feature_json_feature_directory "$repo_root")

scripts/powershell/check-prerequisites.ps1

@@ -56,8 +56,14 @@ EXAMPLES:
 # Source common functions
 . "$PSScriptRoot/common.ps1"
 
-# Get feature paths
-$paths = Get-FeaturePathsEnv
+# Get feature paths.
+# In -PathsOnly mode this is pure resolution, so pass -NoPersist to opt out of
+# the feature.json write side effect (issue #3025).
+if ($PathsOnly) {
+    $paths = Get-FeaturePathsEnv -NoPersist
+} else {
+    $paths = Get-FeaturePathsEnv
+}
 
 # If paths-only mode, output paths and exit (no validation)
 if ($PathsOnly) {

scripts/powershell/common.ps1

@@ -143,6 +143,13 @@ function Save-FeatureJson {
 }
 
 function Get-FeaturePathsEnv {
+    # Read-only callers (e.g. check-prerequisites.ps1 -PathsOnly) pass -NoPersist
+    # so pure path resolution never writes .specify/feature.json, which would
+    # dirty the working tree or overwrite a pinned value (issue #3025).
+    param(
+        [switch]$NoPersist
+    )
+
     $repoRoot = Get-RepoRoot
     $currentBranch = Get-CurrentBranch
 
@@ -157,8 +164,11 @@ function Get-FeaturePathsEnv {
         if (-not [System.IO.Path]::IsPathRooted($featureDir)) {
             $featureDir = Join-Path $repoRoot $featureDir
         }
-        # Persist to feature.json so future sessions without the env var still work
-        Save-FeatureJson -RepoRoot $repoRoot -FeatureDirectory $env:SPECIFY_FEATURE_DIRECTORY
+        # Persist to feature.json so future sessions without the env var still
+        # work - unless the caller opted out for read-only resolution (#3025).
+        if (-not $NoPersist) {
+            Save-FeatureJson -RepoRoot $repoRoot -FeatureDirectory $env:SPECIFY_FEATURE_DIRECTORY
+        }
     } elseif (Test-Path $featureJson) {
         $featureJsonRaw = Get-Content -LiteralPath $featureJson -Raw
         try {

tests/test_check_prerequisites_paths_only.py

@@ -163,6 +163,66 @@ def test_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
     assert result.stdout.strip() == ""
 
 
+@requires_bash
+def test_paths_only_does_not_persist_feature_json(prereq_repo: Path) -> None:
+    """--paths-only must not rewrite feature.json even when the env override
+    differs from the pinned value (#3025).
+
+    Path resolution is read-only, so it must never dirty the working tree or
+    overwrite the persisted feature directory.
+    """
+    pinned = "specs/001-my-feature"
+    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True, exist_ok=True)
+    (prereq_repo / "specs" / "002-other").mkdir(parents=True, exist_ok=True)
+    _write_feature_json(prereq_repo, pinned)
+    fj = prereq_repo / ".specify" / "feature.json"
+    before = fj.read_text(encoding="utf-8")
+
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
+    result = subprocess.run(
+        ["bash", str(script), "--json", "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=env,
+    )
+    assert result.returncode == 0, result.stderr
+    # The override is honored in the output...
+    data = json.loads(result.stdout)
+    assert "002-other" in data["FEATURE_DIR"]
+    # ...but the pinned file on disk is untouched.
+    assert fj.read_text(encoding="utf-8") == before
+
+
+@requires_bash
+def test_normal_mode_still_persists_feature_json(prereq_repo: Path) -> None:
+    """Without --paths-only, the env override is still persisted to feature.json,
+    so the --no-persist opt-out does not regress normal write behavior (#3025)."""
+    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True, exist_ok=True)
+    feat = prereq_repo / "specs" / "002-other"
+    feat.mkdir(parents=True, exist_ok=True)
+    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
+    _write_feature_json(prereq_repo, "specs/001-my-feature")
+    fj = prereq_repo / ".specify" / "feature.json"
+
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=env,
+    )
+    assert result.returncode == 0, result.stderr
+    assert json.loads(fj.read_text(encoding="utf-8"))["feature_directory"] == "specs/002-other"
+
+
 # ── PowerShell tests ──────────────────────────────────────────────────────
 
 
@@ -283,3 +343,32 @@ def test_ps_missing_tasks_error_goes_to_stderr(prereq_repo: Path) -> None:
     assert "tasks.md not found" in result.stderr
     assert "tasks.md not found" not in result.stdout
     assert result.stdout.strip() == ""
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available")
+def test_ps_paths_only_does_not_persist_feature_json(prereq_repo: Path) -> None:
+    """-PathsOnly must not rewrite feature.json even when the env override
+    differs from the pinned value (#3025)."""
+    pinned = "specs/001-my-feature"
+    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True, exist_ok=True)
+    (prereq_repo / "specs" / "002-other").mkdir(parents=True, exist_ok=True)
+    _write_feature_json(prereq_repo, pinned)
+    fj = prereq_repo / ".specify" / "feature.json"
+    before = fj.read_text(encoding="utf-8")
+
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=env,
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "002-other" in data["FEATURE_DIR"]
+    assert fj.read_text(encoding="utf-8") == before