fix(runtime): enforce workspace confinement in one place

"Is this path inside that root" is asked in twenty places in this tree and
answered twenty times by a locally written realpath/commonpath pair. Nine test
files exist because nine call sites each needed their own proof. Each one is
defensible alone; together they are the defect, because the boundary has no
single definition and a site that gets a detail wrong is wrong by itself.

src/path_confinement.py is that definition, and it settles the details the
copies disagreed on. Both sides get canonicalized: comparing a realpath-ed
candidate against a root that was only abspath-ed is the macOS /tmp ->
/private/tmp mismatch that has already produced a false failure here, and
canonicalizing one side is worse than canonicalizing neither. commonpath rather
than startswith, because /a/bc begins with /a/b and is not inside it. A relative
candidate joins the root rather than os.getcwd(), which is whatever directory
the server happens to be running in. NUL and newline are refused with a reason
instead of caught by a bare `except Exception` and reported as an ordinary
escape. Eighteen call sites go through it now. It deliberately does not decide
whether a path is sensitive -- that deny list answers "allowed" rather than
"inside", and it stays with src/tool_execution, which owns it. The one
commonpath left in the tree, in src/workspace_paths.py, stays: that function
translates a host path into a container path, so canonicalizing either side
would change the relative path it computes and break the mapping. It is not a
confinement check.

Two of those sites were weaker than the rest and are fixed rather than moved.
The email attachment check used abspath, which folds `..` but does not resolve
symlinks, so a symlink written into the extraction directory passed it and was
then read through. The skill-reference guard compared a realpath-ed target
against a raw dirname, so on a host where the skills tree is reached through a
symlink the two sides never matched and the guard could not fire.

The execution boundary had two separate holes.

The workspace namespace bound /home and /mnt read-write. On the one platform
where that namespace engages at all, a command inside it reaches outside the
workspace and writes to the user's home directory -- measured by running this
argv on a Linux host with working bubblewrap, not inferred from the source.
Binding the user's whole home directory into a workspace-confinement namespace
gives back most of what the namespace was for. Both are read-only now. The
workspace is also bound writable at its real host path, not only at /workspace:
BashTool's own /tmp redirect rewrites `/tmp/` to `<agent_cwd()>/.tmp/` before
the namespace is built, so the command bwrap receives already names the real
path, and those writes previously landed only because the workspace happened to
sit under the writable /home.

`namespaced or _replace_workspace_alias(...)` chose between a mount namespace
and a regex with nothing in the result saying which one ran. The fallback
rewrites the literal token /workspace in the command string, so a command that
never mentions /workspace is untouched by it and runs on the host unrestricted
-- which is every agent shell command on macOS. Both tools now ask
containment.probe() instead of each deciding for itself, and every bash and
python result carries a containment block naming the mechanism and stating
whether the filesystem dimension actually held. Under enforcing mode the
command is not run and the result says so.

That block reports the filesystem dimension only, and says so in a
reported_dimensions field. The probe knows this host could also give a process
group and a real wall clock, but these two tools still assemble their own
create_subprocess_* call and pass neither, so listing those dimensions would be
exactly the false claim src/containment.py calls worse than an honest absence.

probe() is new on src/containment.py: the same mechanism table and the same
arithmetic as acquire(), stopping before the side effects. acquire() is the
wrong shape for a decision -- it writes a durable grant record, and a record
whose pid is never filled in and whose release() never runs is an entry a
restart reaper keeps finding.

CONTAINMENT_MODE stays report_only. Flipping it refuses every agent shell
command on macOS and on any Linux host without bubblewrap, which is a product
decision rather than a code one.

Smaller things in the same area: the /tmp redirect's makedirs was unguarded, so
a read-only workspace turned a command that merely mentioned `/tmp/` into an
OSError traceback instead of a tool error; it degrades now. WORKSPACE_MOUNT
moved to src/constants.py so the namespace and the path resolvers read one
definition of the contract rather than two. The ".tmp" dirname got a constant,
since it appeared in both tool paths.

One generated artifact moved with it: website/configuration-reference.md pins
the source line where each ODYSSEUS_* variable is read, and three of those
shifted. Regenerated with scripts/generate_env_reference.py; the diff is line
numbers only.

Three existing tests changed. test_workspace_artifact_tool_floor asserted that
an unsafe interpreter prefix produces no `--ro-bind <prefix> <prefix>`, which
now fires on /home because /home is legitimately a read-only base mount.
Asserting the absence of a literal flag string cannot distinguish "the prefix
was rejected" from "the argv mounted that root itself", so it compares the argv
against the no-prefix baseline instead: an unsafe prefix must add nothing.

The Windows bash test asserted dict equality on the
whole result, which makes adding a field to every bash result impossible without
touching a test about tmux; it asserts the shape now. The personal-dir symlink
test grepped the resolver's source for the literal "os.path.realpath", which is
gone because the resolution moved into the shared boundary -- it keeps the
negative assertion that the closure must not grow its own abspath check again,
and the behavioural half now runs against the boundary, where it covers every
call site instead of one closure.

Not verified: the bubblewrap argv is asserted, not executed. There is no bwrap
on macOS, and in Docker it needs --privileged to work at all -- default and
seccomp=unconfined both fail with "Creating new namespace failed", and
--cap-add=SYS_ADMIN fails at pivot_root. The Python tool's
needs_virtual_namespace gate means ordinary Python code gets no namespace even
on a Linux host that could provide one; that is reported now but deliberately
not changed, because it alters the Linux Python path on every call and cannot be
checked from here.

routes/document/document_helpers.py

@@ -13,6 +13,7 @@ from pydantic import BaseModel
 from core.database import Document, DocumentVersion
 from core.database import Session as DbSession
 from src.auth_helpers import _auth_disabled
+from src.path_confinement import is_inside
 from src.upload_handler import UploadHandler
 
 logger = logging.getLogger(__name__)
@@ -136,12 +137,7 @@ _PDF_RENDER_SCALE = 2.0
 
 
 def _upload_path_inside(upload_dir: str, path: str) -> bool:
-    base = os.path.realpath(upload_dir)
-    p = os.path.realpath(path)
-    try:
-        return os.path.commonpath([base, p]) == base
-    except Exception:
-        return False
+    return is_inside(upload_dir, path)
 
 
 def _resolve_user_upload_path(

routes/email/email_routes.py

@@ -39,6 +39,7 @@ from email.mime.multipart import MIMEMultipart
 from fastapi import APIRouter, Query, UploadFile, File, BackgroundTasks, HTTPException, Depends, Request
 from fastapi.responses import FileResponse, StreamingResponse
 from src.constants import DATA_DIR
+from src.path_confinement import confine
 
 from src.llm_core import llm_call_async
 from src.upload_limits import read_upload_limited, EMAIL_COMPOSE_UPLOAD_MAX_BYTES
@@ -4199,9 +4200,12 @@ def setup_email_routes():
                 return {"error": f"Attachment index {index} not found"}
 
             from pathlib import Path as _Path
-            target_root = os.path.abspath(str(target_dir))
-            filepath_str = os.path.abspath(str(filepath))
-            if os.path.commonpath([target_root, filepath_str]) != target_root:
+            # realpath, not abspath: abspath only folds `..`, so a symlink
+            # written into the extraction directory would have passed this
+            # check and then been read through.
+            try:
+                filepath_str = confine(str(target_dir), str(filepath))
+            except (ValueError, OSError):
                 logger.warning("Rejected attachment path outside extraction dir: %s", filepath)
                 return {"error": "Invalid attachment path"}
             filepath = _Path(filepath_str)

routes/gallery/gallery_routes.py

@@ -21,6 +21,7 @@ from src.upload_limits import (
     GALLERY_TRANSFORM_UPLOAD_MAX_BYTES,
 )
 from src.constants import GENERATED_IMAGES_DIR
+from src.path_confinement import confine
 from src.optional_deps import patch_realesrgan_torchvision_compat
 
 from routes.gallery.gallery_helpers import (
@@ -235,12 +236,9 @@ def _gallery_image_path(filename: str) -> Path:
         raise HTTPException(400, "Unsafe gallery filename")
     safe_name = _sanitize_gallery_filename(filename)
     original = str(filename or "")
-    root = GALLERY_IMAGE_DIR.resolve()
-    path = (GALLERY_IMAGE_DIR / safe_name).resolve()
     try:
-        if os.path.commonpath([str(root), str(path)]) != str(root):
-            raise ValueError
-    except Exception:
+        path = Path(confine(GALLERY_IMAGE_DIR, safe_name, allow_root=False))
+    except (ValueError, OSError):
         raise HTTPException(400, "Unsafe gallery filename")
     if safe_name != original:
         raise HTTPException(400, "Unsafe gallery filename")

routes/personal_routes.py

@@ -13,6 +13,7 @@ from core.constants import BASE_DIR, PERSONAL_DIR, PERSONAL_UPLOADS_DIR
 from src.rag_singleton import get_rag_manager
 from src.auth_helpers import require_privilege, require_user
 from core.middleware import require_admin
+from src.path_confinement import confine
 from src.upload_handler import secure_filename
 from src.upload_limits import PERSONAL_UPLOAD_MAX_BYTES
 
@@ -23,10 +24,7 @@ logger = logging.getLogger(__name__)
 def _personal_upload_dir_for_owner(owner: str | None, *, create: bool = True) -> str:
     """Return the per-owner upload directory used for direct RAG uploads."""
     owner_segment = secure_filename((owner or "local").strip())[:80] or "local"
-    upload_dir = os.path.abspath(os.path.join(UPLOADS_DIR, owner_segment))
-    base_abs = os.path.abspath(UPLOADS_DIR)
-    if os.path.commonpath([upload_dir, base_abs]) != base_abs:
-        raise ValueError("Unsafe upload owner path")
+    upload_dir = confine(UPLOADS_DIR, owner_segment, allow_root=False)
     if create:
         os.makedirs(upload_dir, exist_ok=True)
     return upload_dir
@@ -41,10 +39,7 @@ def _unique_personal_upload_path(upload_dir: str, original_name: str | None) ->
     stem, ext = os.path.splitext(safe_name)
     stem = (stem or "upload")[:80]
     filename = f"{stem}-{uuid.uuid4().hex[:10]}{ext.lower()}"
-    file_path = os.path.abspath(os.path.join(upload_dir, filename))
-    upload_abs = os.path.abspath(upload_dir)
-    if os.path.commonpath([file_path, upload_abs]) != upload_abs:
-        raise ValueError("Unsafe upload filename")
+    file_path = confine(upload_dir, filename, allow_root=False)
     return file_path, filename, safe_name
 
 
@@ -167,19 +162,10 @@ def setup_personal_routes(personal_docs_manager, rag_manager, rag_available):
         if not directory:
             raise HTTPException(400, "Directory path is required")
 
-        # realpath (not abspath) so a symlink inside PERSONAL_DIR that points
-        # outside it is resolved before the commonpath confinement check below;
-        # abspath only normalises `..` and would let such a symlink escape.
-        base_abs = os.path.realpath(PERSONAL_DIR)
-        candidate = directory if os.path.isabs(directory) else os.path.join(base_abs, directory)
-        resolved = os.path.realpath(candidate)
         try:
-            in_base = os.path.commonpath([resolved, base_abs]) == base_abs
-        except ValueError:
-            in_base = False
-        if not in_base:
+            return confine(PERSONAL_DIR, directory)
+        except (ValueError, OSError):
             raise HTTPException(403, "Directory must be inside personal documents")
-        return resolved
     
     @router.get("")
     def api_personal_list(owner: str = Depends(require_user), _admin: None = Depends(require_admin)):
@@ -425,17 +411,17 @@ def setup_personal_routes(personal_docs_manager, rag_manager, rag_available):
                 # Scope to the per-owner subdir, not the shared uploads root, so one
                 # admin can't delete another user's personal files by path.
                 deleted_from_disk = False
+                # allow_root=False: the per-owner upload directory itself is
+                # never a deletion target, only files under it.
                 try:
-                    abs_target = os.path.realpath(filepath)
-                    base_abs = os.path.realpath(_personal_upload_dir_for_owner(owner, create=False))
-                    in_uploads = (
-                        abs_target == base_abs
-                        or os.path.commonpath([abs_target, base_abs]) == base_abs
+                    abs_target = confine(
+                        _personal_upload_dir_for_owner(owner, create=False),
+                        filepath,
+                        allow_root=False,
                     )
-                except ValueError:
-                    # commonpath raises on mixed drives / non-comparable paths
-                    in_uploads = False
-                if in_uploads and abs_target != base_abs:
+                except (ValueError, OSError):
+                    abs_target = ""
+                if abs_target:
                     try:
                         os.remove(abs_target)
                         deleted_from_disk = True

routes/upload_routes.py

@@ -24,6 +24,7 @@ from core.database import (
 from src.auth_helpers import effective_user
 from src.attachment_refs import attachment_refs_from_metadata
 from src.constants import GENERATED_IMAGES_DIR
+from src.path_confinement import is_inside
 from src.upload_handler import (
     UploadCleanupSafetyError,
     count_recent_uploads,
@@ -152,10 +153,7 @@ def setup_upload_routes(upload_handler):
         return os.path.realpath(getattr(upload_handler, "upload_dir", UPLOAD_DIR))
 
     def _path_inside_upload_dir(path: str) -> bool:
-        try:
-            return os.path.commonpath([_upload_root(), os.path.realpath(path)]) == _upload_root()
-        except Exception:
-            return False
+        return is_inside(_upload_root(), path)
 
     def _resolve_upload_path(file_id: str) -> str:
         from src.constants import UPLOAD_DIR