diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ba0430d
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+__pycache__/
\ No newline at end of file
diff --git a/ament_cobra/ament_cobra/main.py b/ament_cobra/ament_cobra/main.py
index 2586c01..98f300b 100755
--- a/ament_cobra/ament_cobra/main.py
+++ b/ament_cobra/ament_cobra/main.py
@@ -160,8 +160,30 @@ def main(argv=sys.argv[1:]):
 
     error_count = 0
 
+    # Unfortunately, the CWE ruleset is not outputting a JSON file
+    # Issue submitted here: https://github.com/nimble-code/Cobra/issues/50
+    ruleset_to_filename = {
+        'basic': '_Basic_.txt',
+        'cwe': None,  # No output JSON to work with (need #50 fixed)
+        'p10': '_P10_.txt',
+        'jpl': '_JPL_.txt',
+        'misra2012': '_Misra2012_.txt',
+        'C++/autosar': '_Autosar_.txt',
+    }
+
+    input_filename = ruleset_to_filename[args.ruleset]
+
+    # Remove old input_filename, if it exists.
+    try:
+        os.remove(input_filename)
+    except OSError:
+        pass
+
+    # Temporary file to aggregate results from intermediate `input_filename` files
+    combined_output_filename = "combined_output.txt"
+
     # For each group of files
-    for group_name in sorted(groups.keys()):
+    for i,group_name in enumerate(sorted(groups.keys())):
         files_in_group = groups[group_name]
 
         # If a compile_commands.json is provided, process each source file
@@ -173,14 +195,23 @@ def main(argv=sys.argv[1:]):
                 else:
                     arguments = cmd + [filename]
 
+                # Invoke cobra, and aggregate its output
                 error_count += invoke_cobra(arguments, args.verbose)
+                combine_output(input_filename, combined_output_filename, first=(i==0), verbose=args.verbose)
+
         # Otherwise, run Cobra on this group of files
         else:
             arguments = cmd
             for include_dir in (args.include_dirs or []):
                 cmd.extend(['-I' + include_dir])
             arguments.extend(files_in_group)
+
+            # Invoke cobra, and aggregate its output
             error_count += invoke_cobra(arguments, args.verbose)
+            combine_output(input_filename, combined_output_filename, first=(i==0), verbose=args.verbose)
+    
+    # Move the temporary combined output into the expected final location
+    os.rename(combined_output_filename, input_filename)
 
     # Output a summary
     if not error_count:
@@ -190,19 +221,6 @@ def main(argv=sys.argv[1:]):
         print('%d errors' % error_count, file=sys.stderr)
         rc = 1
 
-    # Unfortunately, the CWE ruleset is not outputting a JSON file
-    # Issue submitted here: https://github.com/nimble-code/Cobra/issues/50
-    ruleset_to_filename = {
-        'basic': '_Basic_.txt',
-        'cwe': None,  # No output JSON to work with (need #50 fixed)
-        'p10': '_P10_.txt',
-        'jpl': '_JPL_.txt',
-        'misra2012': '_Misra2012_.txt',
-        'C++/autosar': '_Autosar_.txt',
-    }
-
-    input_filename = ruleset_to_filename[args.ruleset]
-
     if (args.xunit_file or args.sarif_file) and input_filename is None:
         # When using the CWE ruleset, Cobra doesn't generate an output file
         print(
@@ -223,14 +241,26 @@ def main(argv=sys.argv[1:]):
         else:
             # Generate the xunit output file
             if args.xunit_file:
-                write_output_file(input_filename, '-junit', args.xunit_file)
+                write_output_file(input_filename, ['-junit'], args.xunit_file)
 
             # Generate the SARIF output file
             if args.sarif_file:
-                write_output_file(input_filename, '-sarif', args.sarif_file)
+                write_output_file(input_filename, ['-sarif','-a'], args.sarif_file)
 
     return rc
 
+def combine_output(input_filename, output_filename, first=False, verbose=False):
+    '''
+    Appends the contents of `input_filename` into `output_filename`. Used to aggregate Cobra output.
+    '''
+    if verbose:
+        print(f"Appending {input_filename} to {output_filename}")
+    with open(output_filename, "a") as out:
+        with open(input_filename, "r") as in_f:
+            # If this isn't the first file, we need to prepend a `,` to form valid json
+            if not first: out.write(",")
+
+            out.write(in_f.read())
 
 def find_executable(file_name, additional_paths=None):
     path = None
@@ -372,10 +402,10 @@ def get_input_filenames(groups):
     return filenames
 
 
-def write_output_file(input_filename, conversion_flag, output_filename):
-    folder_name = os.path.basename(os.path.dirname(output_filename))
+def write_output_file(input_filename, flags, output_filename):
+
     try:
-        cmd = ['json_convert', conversion_flag, '-f', input_filename]
+        cmd = ['json_convert', '-f', input_filename] + flags
         p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
         cmd_output = p.communicate()[0]
         with open(output_filename, 'w') as f:
diff --git a/cobra_vendor/CMakeLists.txt b/cobra_vendor/CMakeLists.txt
index 7399af0..b9725db 100644
--- a/cobra_vendor/CMakeLists.txt
+++ b/cobra_vendor/CMakeLists.txt
@@ -11,7 +11,7 @@ endif()
 
 # The Cobra source code version/revision numbers
 set(VER "4.1")
-set(REV "09a5e421bfa7b84d5fca651d3ae3a93e7c30389f")
+set(REV "81fba6ac6b734b0dd74f464e8501581040e5f02f")
 
 include(ExternalProject)
 ExternalProject_Add(cobra-${VER}