fix(workbench): bind finding excerpts to selected source paths

sdk/typescript/README.md

@@ -45,6 +45,11 @@ make one extra model call, even with a cost limit.
 Keep results outside the repository and restrict access: reports can contain
 source code, vulnerability details, and reproduction steps.
 
+Saved-history excerpts use scanned Git objects without fetching missing data.
+Working-tree diff scans omit excerpts, as do historical scans whose source or
+scope cannot be established. Unambiguous older scans remain readable. An omitted
+excerpt does not remove the finding.
+
 ### Validate an existing finding
 
 ```ts

sdk/typescript/_bundled_plugin/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "codex-security",
-  "version": "0.1.60",
+  "version": "0.1.65",
   "description": "Codex Security workflows for security scans, analysis, and investigation.",
   "author": {
     "name": "OpenAI"

sdk/typescript/_bundled_plugin/scripts/deep_scan_workbench.py

@@ -21,6 +21,7 @@
 from filesystem_identity import serialize_filesystem_identity
 from finalize_scan_contract import _read_scan_local_json
 from workbench.handoff import require_current_continuation
+from workbench_source_scopes import capture_source_scopes
 from workbench_target import (
     directory_content_digest,
     directory_snapshot_regular_file_count,
@@ -823,6 +824,11 @@ def begin_deep_scan_for_target(
                 terminal["id"],
                 start_disposition="joined",
             )
+        source_scopes = capture_source_scopes(
+            target,
+            (revision, target_snapshot_digest, target_device, target_inode),
+            [scope],
+        )
         config = effective_deep_scan_config(args)
         workflow_version = optional_text(args.workflow_version, maximum=256)
         if workflow_version is None:
@@ -870,10 +876,10 @@ def begin_deep_scan_for_target(
             """
             INSERT INTO scans (
                 id, workspace_id, target_id, target_path, target_revision, target_snapshot_digest,
-                target_device, target_inode, scope, mode, user_context,
+                target_device, target_inode, source_scopes_json, scope, mode, user_context,
                 deep_scan_owner_thread_id, scan_dir, model, reasoning_effort, status, phase,
                 handoff_status, started_at, created_at, updated_at
-            ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, 'deep', ?, ?, ?, ?, ?,
+            ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 'deep', ?, ?, ?, ?, ?,
                 'running', 'preflight', 'delivered', ?, ?, ?)
             """,
             (
@@ -885,6 +891,7 @@ def begin_deep_scan_for_target(
                 target_snapshot_digest,
                 target_device,
                 target_inode,
+                json.dumps(source_scopes),
                 scope,
                 user_context,
                 thread_id,

sdk/typescript/_bundled_plugin/scripts/workbench_db.py

@@ -101,7 +101,8 @@
 from workbench_schema import (
     sql_statements as sql_statements,
 )
-from workbench_source_excerpt import finding_source_excerpt, safe_source_path
+from workbench_source_excerpt import finding_source_excerpt
+from workbench_source_scopes import capture_source_scopes, safe_source_path
 from workbench_target import (
     clean_worktree_content_digest,
     copy_directory_excluding,
@@ -444,6 +445,12 @@ def requested_scan_paths(scan: sqlite3.Row) -> list[str]:
     return [scan["scope"]]
 
 
+def public_scan_recipe(scan: sqlite3.Row) -> dict[str, Any]:
+    recipe = json.loads(scan["recipe_json"], parse_constant=reject_non_finite_json)
+    recipe.pop("_codexSecurityFileScopes", None)
+    return recipe
+
+
 def scan_contract(scan: sqlite3.Row) -> dict[str, Any]:
     target = Path(scan["target_path"])
     target_contract = {
@@ -849,6 +856,12 @@ def start_scan(connection: sqlite3.Connection, args: argparse.Namespace) -> dict
             diff_target,
             metadata=target_metadata,
         )
+        source_scopes = capture_source_scopes(
+            target,
+            target_identity,
+            [scope],
+            diff_target_kind=diff_target["kind"] if diff_target is not None else None,
+        )
         target_root = scan_target_root(args.scan_root, target)
         target_root.mkdir(parents=True, exist_ok=True)
         if manages_transaction:
@@ -897,6 +910,7 @@ def start_scan(connection: sqlite3.Connection, args: argparse.Namespace) -> dict
             scope=scope,
             diff_target=diff_target,
             target_identity=target_identity,
+            source_scopes=source_scopes,
             target_root=target_root,
             target_summary=target_summary,
             scope_file_count=scope_file_count,
@@ -953,6 +967,12 @@ def _start_prompt_driven_scan(
     )
     diff_identity = scan_diff_identity(diff_target)
     target_identity = scan_target_identity(target, diff_target)
+    source_scopes = capture_source_scopes(
+        target,
+        target_identity,
+        [scope],
+        diff_target_kind=diff_target["kind"] if diff_target is not None else None,
+    )
     target_root = scan_target_root(args.scan_root, target)
 
     connection.execute("BEGIN IMMEDIATE")
@@ -1052,6 +1072,7 @@ def _start_prompt_driven_scan(
             scope=scope,
             diff_target=diff_target,
             target_identity=target_identity,
+            source_scopes=source_scopes,
             target_root=target_root,
             target_summary=target_summary,
             scope_file_count=scope_file_count,
@@ -1660,6 +1681,7 @@ def register_cli_scan(connection: sqlite3.Connection, args: argparse.Namespace)
     recipe = parse_scan_recipe(recipe_json, repository)
     requested_target = recipe["target"]
     paths = requested_target["paths"]
+    recipe.pop("_codexSecurityFileScopes", None)
     scope = paths[0] if len(paths) == 1 else "."
     diff_target = None
     if requested_target["kind"] in {"refs", "working_tree"}:
@@ -1677,6 +1699,12 @@ def register_cli_scan(connection: sqlite3.Connection, args: argparse.Namespace)
             diff_target["contentDigest"] = worktree_content_digest(repository)
     mode = "diff" if diff_target is not None else recipe["mode"]
     target_identity = scan_target_identity(repository, diff_target)
+    source_scopes = capture_source_scopes(
+        repository,
+        target_identity,
+        paths or ["."],
+        diff_target_kind=diff_target["kind"] if diff_target is not None else None,
+    )
     scope_file_count = (
         directory_snapshot_regular_file_count(repository)
         if not paths
@@ -1734,6 +1762,7 @@ def register_cli_scan(connection: sqlite3.Connection, args: argparse.Namespace)
             scope=scope,
             diff_target=diff_target,
             target_identity=target_identity,
+            source_scopes=source_scopes,
             target_root=scan_dir.parent,
             target_summary=None,
             scope_file_count=scope_file_count,
@@ -1744,7 +1773,9 @@ def register_cli_scan(connection: sqlite3.Connection, args: argparse.Namespace)
         connection.execute(
             "UPDATE scans SET recipe_json = ?, parent_scan_id = ?, user_context = ? WHERE id = ?",
             (
-                json.dumps(recipe, allow_nan=False, separators=(",", ":"), sort_keys=True),
+                json.dumps(
+                    recipe, allow_nan=False, separators=(",", ":"), sort_keys=True
+                ),
                 parent_scan_id,
                 user_context,
                 scan_id,
@@ -1832,7 +1863,7 @@ def get_scan_recipe(connection: sqlite3.Connection, args: argparse.Namespace) ->
         raise SystemExit("This scan does not have a saved launch recipe.")
     return {
         "parentScanId": scan["parent_scan_id"],
-        "recipe": json.loads(scan["recipe_json"], parse_constant=reject_non_finite_json),
+        "recipe": public_scan_recipe(scan),
         "scanId": scan["id"],
     }
 
@@ -3157,7 +3188,7 @@ def scan_context(
     }
     if scan["recipe_json"] is not None:
         context["parentScanId"] = scan["parent_scan_id"]
-        context["recipe"] = json.loads(scan["recipe_json"], parse_constant=reject_non_finite_json)
+        context["recipe"] = public_scan_recipe(scan)
     return context
 
 
@@ -3443,6 +3474,7 @@ def finding_result(
     severity = details.get("severity")
     severity = severity if isinstance(severity, dict) else {}
     locations = []
+    excerpt_locations = []
     try:
         target = require_scan_target_identity(scan)
     except SystemExit:
@@ -3457,6 +3489,14 @@ def finding_result(
         """,
         (occurrence["id"], FINDING_LOCATIONS_LIMIT),
     ):
+        excerpt_locations.append(
+            {
+                "endLine": row["end_line"],
+                "path": row["relative_path"],
+                "role": row["role"],
+                "startLine": row["start_line"],
+            }
+        )
         absolute_path = safe_source_path(target, row["relative_path"]) if target else None
         location = {
             "endLine": row["end_line"],
@@ -3501,7 +3541,9 @@ def finding_result(
         result["knownSince"] = known_since
         result["knownScanIds"] = known_scan_ids
     result.pop("artifactPaths", None)
-    source_excerpt = finding_source_excerpt(scan, target, locations)
+    source_excerpt = finding_source_excerpt(
+        scan, target, excerpt_locations, requested_scan_paths(scan)
+    )
     if source_excerpt:
         result["sourceExcerpt"] = source_excerpt
     artifact_paths = finding_artifact_paths(Path(scan["scan_dir"]), details)

sdk/typescript/_bundled_plugin/scripts/workbench_scan_start.py

@@ -11,6 +11,7 @@
 from collections.abc import Callable
 from datetime import datetime, timezone
 from pathlib import Path
+from typing import Any
 
 # Some plugin hosts launch Python with safe-path isolation enabled.
 sys.path.insert(0, str(Path(__file__).resolve().parent))
@@ -157,6 +158,7 @@ def insert_running_scan(
     scope: str,
     diff_target: dict[str, str] | None,
     target_identity: tuple[str, str | None, int | str, int | str],
+    source_scopes: dict[str, Any],
     target_root: Path,
     target_summary: str | None,
     scope_file_count: int,
@@ -180,11 +182,11 @@ def insert_running_scan(
         """
         INSERT INTO scans (
             id, workspace_id, target_id, target_path, target_revision, target_snapshot_digest,
-            target_device, target_inode, scope, mode, user_context,
+            target_device, target_inode, source_scopes_json, scope, mode, user_context,
             deep_scan_owner_thread_id, diff_target_kind, diff_base_revision,
             diff_head_revision, diff_content_digest, target_summary, scan_dir, model,
             reasoning_effort, status, phase, handoff_status, started_at, created_at, updated_at
-        ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
+        ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
             'running', 'preflight', ?, ?, ?, ?)
         """,
         (
@@ -193,6 +195,9 @@ def insert_running_scan(
             workspace["target_id"],
             str(target),
             *target_identity,
+            json.dumps(
+                source_scopes, allow_nan=False, separators=(",", ":"), sort_keys=True
+            ),
             scope,
             workspace["default_mode"],
             user_context,

sdk/typescript/_bundled_plugin/scripts/workbench_schema.py

@@ -697,6 +697,13 @@
         ALTER TABLE deep_scan_runs ADD COLUMN publication_error_message TEXT;
         """,
     ),
+    (
+        34,
+        "persist authorized source excerpt scopes",
+        """
+        ALTER TABLE scans ADD COLUMN source_scopes_json TEXT;
+        """,
+    ),
 )
 
 
@@ -772,11 +779,15 @@ def apply_migrations(
                         "publication_error_message",
                         "TEXT",
                     )
+                elif version == 34:
+                    add_column_if_missing(connection, "scans", "source_scopes_json", "TEXT")
                 continue
             if version == 6:
                 repair_thread_scoped_workspaces_migration(connection)
             elif version == 16:
                 should_backfill_targets = repair_stable_targets_migration(connection)
+            elif version == 34:
+                add_column_if_missing(connection, "scans", "source_scopes_json", "TEXT")
             else:
                 for statement in sql_statements(sql):
                     connection.execute(statement)
@@ -911,6 +922,17 @@ def normalize_pre_release_execution_profile_migrations(
 
 
 def normalize_pre_release_migrations(connection: sqlite3.Connection, timestamp: str) -> None:
+    source_scope_migration = connection.execute(
+        "SELECT name FROM schema_migrations WHERE version = 34"
+    ).fetchone()
+    if (
+        source_scope_migration is not None
+        and source_scope_migration["name"] != "persist authorized source excerpt scopes"
+    ):
+        raise SystemExit(
+            "The Codex Security database has an unsupported source-scope migration history."
+        )
+
     completion_warning_migration = connection.execute(
         "SELECT name FROM schema_migrations WHERE version = 25"
     ).fetchone()