fix(#1625): exclude agent working directories from git tracking

internal/cli/run.go

@@ -43,6 +43,14 @@ const (
 	maxContextScanDepth = 5
 )
 
+// agentWorkingDirExcludes lists directory patterns that agents may create
+// during execution but must never commit. These are added to
+// .git/info/exclude before the agent runs so git ignores them entirely.
+var agentWorkingDirExcludes = []string{
+	".agentready/",
+	".fullsend-workspace/",
+}
+
 func newRunCmd() *cobra.Command {
 	var fullsendDir string
 	var outputBase string
@@ -450,6 +458,14 @@ func runAgent(ctx context.Context, agentName, fullsendDir, outputBase, targetRep
 		}
 	}
 
+	// 8a-2. Exclude agent working directories from git tracking.
+	// Agents may create working directories (e.g. .agentready/) during
+	// execution. These must never appear in commits. Adding them to
+	// .git/info/exclude ensures git status/add ignores them entirely.
+	if err := excludeAgentWorkingDirs(sandboxName, repoDir, printer); err != nil {
+		printer.StepWarn("Could not exclude agent working dirs: " + err.Error())
+	}
+
 	// 8b. Copy agent-input files (if configured).
 	if h.AgentInput != "" {
 		inputStart := time.Now()
@@ -1248,6 +1264,25 @@ func relOrAbs(base, path string) string {
 	return rel
 }
 
+// excludeAgentWorkingDirs adds agent working directory patterns to
+// .git/info/exclude so they are invisible to git status and git add.
+func excludeAgentWorkingDirs(sandboxName, repoDir string, printer *ui.Printer) error {
+	var lines []string
+	for _, pattern := range agentWorkingDirExcludes {
+		lines = append(lines, pattern)
+	}
+	if len(lines) == 0 {
+		return nil
+	}
+	payload := strings.Join(lines, "\n")
+	excludeCmd := fmt.Sprintf("printf '%%s\\n' '%s' >> %s/.git/info/exclude",
+		payload, repoDir)
+	if _, _, _, err := sandbox.Exec(sandboxName, excludeCmd, 5*time.Second); err != nil {
+		return fmt.Errorf("writing git exclude: %w", err)
+	}
+	return nil
+}
+
 // hasAgentsMD checks whether the repo directory contains an AGENTS.md file
 // in any common casing.
 func hasAgentsMD(repoDir string) bool {

internal/cli/run_test.go

@@ -582,6 +582,26 @@ func TestResolveLinuxBinary_Download(t *testing.T) {
 	assert.NoError(t, validateLinuxBinary(binPath), "downloaded binary should be a valid Linux/amd64 ELF")
 }
 
+func TestAgentWorkingDirExcludes_ContainsKnownPatterns(t *testing.T) {
+	// Verify the exclusion list contains the known agent working directories.
+	expected := []string{".agentready/", ".fullsend-workspace/"}
+	for _, pattern := range expected {
+		found := false
+		for _, exclude := range agentWorkingDirExcludes {
+			if exclude == pattern {
+				found = true
+				break
+			}
+		}
+		assert.True(t, found, "agentWorkingDirExcludes should contain %q", pattern)
+	}
+}
+
+func TestAgentWorkingDirExcludes_NotEmpty(t *testing.T) {
+	assert.NotEmpty(t, agentWorkingDirExcludes,
+		"agentWorkingDirExcludes must not be empty — agents create working dirs that need exclusion")
+}
+
 func TestReadOIDCAuthFile_Success(t *testing.T) {
 	f := filepath.Join(t.TempDir(), "auth")
 	require.NoError(t, os.WriteFile(f, []byte("bearer test-token"), 0o600))

internal/scaffold/fullsend-repo/scripts/post-code-test.sh

@@ -539,6 +539,85 @@ run_error_comment_test "error-comment-non-org-mode-fallback" \
   "https://github.com/my-org/my-repo/actions/runs/67890" "yes" \
   ""
 
+# ---------------------------------------------------------------------------
+# Test helper — reimplements the agent artifact stripping logic from
+# post-code.sh section 2b. Given a list of changed files, returns which
+# files would be stripped as agent artifacts.
+# ---------------------------------------------------------------------------
+strip_agent_artifacts() {
+  local changed_files="$1"
+  local agent_artifact_patterns=".agentready/ .fullsend-workspace/"
+  local stripped=""
+
+  for file in ${changed_files}; do
+    local is_artifact=false
+    for pattern in ${agent_artifact_patterns}; do
+      local dir="${pattern%/}"
+      case "${file}" in
+        "${dir}"/*|"${dir}") is_artifact=true; break ;;
+        */"${dir}"/*|*/"${dir}") is_artifact=true; break ;;
+      esac
+    done
+    if [ "${is_artifact}" = "true" ]; then
+      stripped="${stripped} ${file}"
+    fi
+  done
+
+  echo "${stripped}" | xargs
+}
+
+run_artifact_test() {
+  local test_name="$1"
+  local changed_files="$2"
+  local expected_stripped="$3"
+
+  local actual
+  actual="$(strip_agent_artifacts "${changed_files}")"
+
+  if [ "${actual}" != "${expected_stripped}" ]; then
+    echo "FAIL: ${test_name}"
+    echo "  changed_files:     '${changed_files}'"
+    echo "  expected stripped: '${expected_stripped}'"
+    echo "  actual stripped:   '${actual}'"
+    FAILURES=$((FAILURES + 1))
+    return
+  fi
+
+  echo "PASS: ${test_name}"
+}
+
+# --- Agent artifact stripping test cases ---
+
+# .agentready/ files should be stripped
+run_artifact_test "strip-agentready-file" \
+  ".agentready/assessment.json src/main.go" \
+  ".agentready/assessment.json"
+
+# .fullsend-workspace/ files should be stripped
+run_artifact_test "strip-fullsend-workspace-file" \
+  ".fullsend-workspace/scratch.txt src/main.go" \
+  ".fullsend-workspace/scratch.txt"
+
+# Nested paths should also be stripped
+run_artifact_test "strip-nested-agentready" \
+  "subdir/.agentready/data.json src/main.go" \
+  "subdir/.agentready/data.json"
+
+# Normal files should not be stripped
+run_artifact_test "keep-normal-files" \
+  "src/main.go internal/handler.go" \
+  ""
+
+# Multiple artifacts stripped together
+run_artifact_test "strip-multiple-artifacts" \
+  ".agentready/a.json .fullsend-workspace/b.txt src/main.go" \
+  ".agentready/a.json .fullsend-workspace/b.txt"
+
+# Empty input should produce no stripping
+run_artifact_test "strip-empty-input" \
+  "" \
+  ""
+
 # --- Summary ---
 
 echo ""

internal/scaffold/fullsend-repo/scripts/post-code.sh

@@ -126,6 +126,59 @@ fi
 echo "Changed files:"
 echo "${CHANGED_FILES}" | sed 's/^/  /'
 
+# ---------------------------------------------------------------------------
+# 2b. Strip agent working directories (defense-in-depth)
+#
+# Agent working dirs (.agentready/, .fullsend-workspace/) should never
+# appear in commits. The harness excludes them via .git/info/exclude, but
+# if an agent manages to stage them anyway, strip them here before push.
+# ---------------------------------------------------------------------------
+AGENT_ARTIFACT_PATTERNS=".agentready/ .fullsend-workspace/"
+STRIPPED_FILES=""
+for file in ${CHANGED_FILES}; do
+  is_artifact=false
+  for pattern in ${AGENT_ARTIFACT_PATTERNS}; do
+    dir="${pattern%/}"  # strip trailing slash for prefix matching
+    case "${file}" in
+      "${dir}"/*|"${dir}") is_artifact=true; break ;;
+      */"${dir}"/*|*/"${dir}") is_artifact=true; break ;;
+    esac
+  done
+  if [ "${is_artifact}" = "true" ]; then
+    echo "::warning::Stripping agent artifact from commit: ${file}"
+    STRIPPED_FILES="${STRIPPED_FILES} ${file}"
+  fi
+done
+
+if [ -n "${STRIPPED_FILES}" ]; then
+  echo "::warning::Agent committed working directory artifacts — stripping before push"
+  # shellcheck disable=SC2086
+  git rm --cached --quiet ${STRIPPED_FILES}
+  git commit --amend --no-edit
+
+  # Rebuild CHANGED_FILES without the stripped artifacts.
+  CLEAN_FILES=""
+  for file in ${CHANGED_FILES}; do
+    is_stripped=false
+    for sf in ${STRIPPED_FILES}; do
+      if [ "${file}" = "${sf}" ]; then
+        is_stripped=true
+        break
+      fi
+    done
+    if [ "${is_stripped}" = "false" ]; then
+      CLEAN_FILES="${CLEAN_FILES}${CLEAN_FILES:+
+}${file}"
+    fi
+  done
+  CHANGED_FILES="${CLEAN_FILES}"
+
+  if [ -z "${CHANGED_FILES}" ]; then
+    echo "::notice::All changed files were agent artifacts — nothing to push"
+    exit 0
+  fi
+fi
+
 # ---------------------------------------------------------------------------
 # 3. Authoritative secret scan
 # ---------------------------------------------------------------------------