diff --git a/.evergreen/scripts/resync-all-specs.py b/.evergreen/scripts/resync-all-specs.py
index 8e58e56da2..1996d5d634 100644
--- a/.evergreen/scripts/resync-all-specs.py
+++ b/.evergreen/scripts/resync-all-specs.py
@@ -6,7 +6,6 @@
 import subprocess
 from argparse import Namespace
 from subprocess import CalledProcessError
-from typing import Optional
 
 
 def resync_specs(directory: pathlib.Path, errored: dict[str, str]) -> None:
@@ -32,14 +31,27 @@ def resync_specs(directory: pathlib.Path, errored: dict[str, str]) -> None:
 
 def apply_patches(errored):
     print("Beginning to apply patches")
-    subprocess.run(["bash", "./.evergreen/remove-unimplemented-tests.sh"], check=True)  # noqa: S603, S607
+    subprocess.run(
+        ["bash", "./.evergreen/remove-unimplemented-tests.sh"],  # noqa: S603, S607
+        check=True,
+    )
     try:
-        subprocess.run(
-            ["git apply -R --allow-empty --whitespace=fix ./.evergreen/spec-patch/*"],  # noqa: S607
-            shell=True,  # noqa: S602
-            check=True,
-            stderr=subprocess.PIPE,
-        )
+        # Avoid shell=True by passing arguments as a list.
+        # Note: glob expansion doesn't work in shell=False, so we use a list of files.
+        patches = [str(p) for p in pathlib.Path("./.evergreen/spec-patch/").glob("*")]
+        if patches:
+            subprocess.run(
+                [  # noqa: S603, S607
+                    "git",
+                    "apply",
+                    "-R",
+                    "--allow-empty",
+                    "--whitespace=fix",
+                    *patches,
+                ],
+                check=True,
+                stderr=subprocess.PIPE,
+            )
     except CalledProcessError as exc:
         errored["applying patches"] = exc.stderr
 
@@ -73,17 +85,24 @@ def check_new_spec_directories(directory: pathlib.Path) -> list[str]:
     return list(spec_set - test_set)
 
 
-def write_summary(errored: dict[str, str], new: list[str], filename: Optional[str]) -> None:
+def write_summary(errored: dict[str, str], new: list[str], filename: str | None) -> None:
     """Generate the PR description"""
     pr_body = ""
+    # Avoid shell=True and complex pipes by using Python to process git output
     process = subprocess.run(
-        ["git diff --name-only | awk -F'/' '{print $2}' | sort | uniq"],  # noqa: S607
-        shell=True,  # noqa: S602
+        ["git", "diff", "--name-only"],  # noqa: S603, S607
         capture_output=True,
         text=True,
         check=True,
     )
-    succeeded = process.stdout.strip().split()
+    changed_files = process.stdout.strip().splitlines()
+    succeeded_set = set()
+    for f in changed_files:
+        parts = f.split("/")
+        if len(parts) > 1:
+            succeeded_set.add(parts[1])
+    succeeded = sorted(succeeded_set)
+
     if len(succeeded) > 0:
         pr_body += "The following specs were changed:\n -"
         pr_body += "\n -".join(succeeded)
@@ -120,7 +139,9 @@ def main(args: Namespace):
         description="Python Script to resync all specs and generate summary for PR."
     )
     parser.add_argument(
-        "--filename", help="Name of file for the summary to be written into.", default=None
+        "--filename",
+        help="Name of file for the summary to be written into.",
+        default=None,
     )
     args = parser.parse_args()
     main(args)
diff --git a/doc/conf.py b/doc/conf.py
index 063429cd98..6d648ca503 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -88,6 +88,8 @@
 linkcheck_ignore = [
     "https://github.com/mongodb/specifications/blob/master/source/server-discovery-and-monitoring/server-monitoring.md#requesting-an-immediate-check",
     "https://github.com/mongodb/specifications/blob/master/source/transactions-convenient-api/transactions-convenient-api.md#handling-errors-inside-the-callback",
+    "https://github.com/mongodb/specifications/blob/master/source/uri-options/uri-options.md",
+    "https://github.com/mongodb/specifications/blob/master/source/uri-options/uri-options.md",
     "https://github.com/mongodb/libmongocrypt/blob/master/bindings/python/README.rst#installing-from-source",
     r"https://wiki.centos.org/[\w/]*",
     r"https://sourceforge.net/",
@@ -186,8 +188,8 @@
     ("index", "PyMongo.tex", "PyMongo Documentation", "Michael Dirolf", "manual"),
 ]
 
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
+# The name of an image file (relative to this directory) to place at the top
+# of the title page.
 # latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,