fix: harden agent worktree indexing and structural edit planning

.sentrux/baseline.json

@@ -5,18 +5,18 @@
   },
   "metrics": {
     "complex_fn_count": 12,
-    "coupling_score": 44.78,
-    "cross_module_edges": 918,
+    "coupling_score": 45.07,
+    "cross_module_edges": 1023,
     "cycle_count": 0,
-    "files": 205,
-    "functions": 2804,
+    "files": 227,
+    "functions": 3060,
     "god_file_count": 29,
     "max_complexity": 162,
-    "quality_signal": 3971,
-    "total_import_edges": 918
+    "quality_signal": 3969,
+    "total_import_edges": 1023
   },
-  "savedAt": 1784946137,
+  "savedAt": 1785048977,
   "schema": "code-intel-sentrux-baseline.v2",
   "scope": ".",
-  "sourceCommit": "e746956754ff0dc89ae97d03716c7f53b967aa33"
+  "sourceCommit": "d20e4476c68c34b9596d96dfa7895dceabbd21b4"
 }

.sentrux/rules.toml

@@ -7,10 +7,14 @@
 # no god files, coupling grade B) is tracked modernization debt
 # (issue #14, "Remaining tracked debt").
 #
-# Measured ratchet evidence (sentrux-native 2.0.0, 2026-07-25, PR #15 tree,
-# recorded together with .sentrux/baseline.json in the same commit):
+# Measured ratchet evidence (sentrux-native 2.0.0, 2026-07-26, PR #39 tree
+# merged with v0.6.0 main, recorded together with .sentrux/baseline.json in
+# the same commit):
 #   max_complexity 162 (scripts/tests/test-code-intel-pipeline.ps1),
-#   god_file_count 29, coupling_score 44.78, cycle_count 0.
+#   god_file_count 29, coupling_score 45.07, cycle_count 0.
+# The 44.78 -> 45.07 coupling and 3971 -> 3969 quality movement is the cost
+# of the v0.6.0 audit layer plus the edit.ast-grep-plan adapter module; god
+# files and cycles did not move.
 # The previous B / 70 / no-god thresholds were never green under any engine:
 # the first honest self-scan of v0.5.0 already failed all three, so restoring
 # them would guarantee a permanently red release gate, not protection.

crates/code-intel-cli/src/capability_inventory.rs

@@ -29,6 +29,8 @@ mod native_code_evidence;
 mod project_orientation;
 #[path = "project_orientation_benchmark.rs"]
 mod project_orientation_benchmark;
+#[path = "structured_edit.rs"]
+mod structured_edit;
 #[path = "understanding_quadrant.rs"]
 mod understanding_quadrant;
 
@@ -71,6 +73,7 @@ pub(crate) fn execute(
         "evidence.native-code.compat" => {
             native_code_evidence::execute(request, verified_inputs, out)
         }
+        "edit.ast-grep-plan.compat" => structured_edit::execute(request, verified_inputs, out),
         "project.orientation.compat" => project_orientation::execute(request, verified_inputs, out),
         "understanding.quadrant.compat" => {
             understanding_quadrant::execute(request, verified_inputs, out)
@@ -315,7 +318,7 @@ fn inventory(request: &Value, out: &Path) -> Result<AdapterOutput, AdapterError>
         .collect::<Vec<_>>();
     baseline_globs.extend(
         lease
-            .inventory_gitlink_paths()
+            .inventory_excluded_paths()
             .iter()
             .map(|path| gitlink_exclude_glob(path)),
     );

crates/code-intel-cli/src/snapshot.rs

@@ -350,6 +350,7 @@ pub(crate) struct SnapshotLease {
     policy: Policy,
     scopes: Vec<String>,
     manifest: InputManifest,
+    inventory_excluded_paths: Vec<String>,
 }
 
 #[derive(Clone, Debug, PartialEq, Eq)]
@@ -466,11 +467,20 @@ pub(crate) fn begin_consumption(repo: &Path, expected: &Value) -> Result<Snapsho
     }
     let manifest =
         input_manifest(repo, policy, &scopes).map_err(|error| error.message().to_string())?;
+    let inventory_excluded_paths = if git_context(repo)
+        .map_err(|error| error.message().to_string())?
+        .is_some()
+    {
+        untracked_directory_paths(repo, &scopes).map_err(|error| error.message().to_string())?
+    } else {
+        Vec::new()
+    };
     Ok(SnapshotLease {
         expected: expected.clone(),
         policy,
         scopes,
         manifest,
+        inventory_excluded_paths,
     })
 }
 
@@ -490,12 +500,13 @@ impl SnapshotLease {
         paths
     }
 
-    pub(crate) fn inventory_gitlink_paths(&self) -> Vec<String> {
+    pub(crate) fn inventory_excluded_paths(&self) -> Vec<String> {
         self.manifest
             .entries
             .iter()
             .filter(|entry| entry.kind == "gitlink")
             .map(|entry| entry.path.clone())
+            .chain(self.inventory_excluded_paths.iter().cloned())
             .collect()
     }
 
@@ -1069,7 +1080,7 @@ fn effective_file_mode(index_mode: &str, metadata: &fs::Metadata) -> String {
     }
 }
 
-fn untracked_paths(repo: &Path, scopes: &[String]) -> Result<Vec<String>, SnapshotError> {
+fn untracked_entries(repo: &Path, scopes: &[String]) -> Result<Vec<String>, SnapshotError> {
     let mut args = vec![
         "ls-files",
         "--others",
@@ -1085,6 +1096,20 @@ fn untracked_paths(repo: &Path, scopes: &[String]) -> Result<Vec<String>, Snapsh
     )?)
 }
 
+fn untracked_paths(repo: &Path, scopes: &[String]) -> Result<Vec<String>, SnapshotError> {
+    Ok(untracked_entries(repo, scopes)?
+        .into_iter()
+        .filter(|path| !path.ends_with('/'))
+        .collect())
+}
+
+fn untracked_directory_paths(repo: &Path, scopes: &[String]) -> Result<Vec<String>, SnapshotError> {
+    Ok(untracked_entries(repo, scopes)?
+        .into_iter()
+        .filter_map(|path| path.strip_suffix('/').map(str::to_string))
+        .collect())
+}
+
 #[derive(Clone, Debug, Default, PartialEq, Eq)]
 struct Overlay {
     tracked_modified: BTreeSet<String>,