diff --git a/.gitignore b/.gitignore
index bd0c70ff..a7a3c32d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,10 +9,8 @@ coverage
 cache
 test/integration/.start-translator
 regression/output/*-*
-regression/connectathon
-regression/coverage-script-bundles
-regression/ecqm-content-r4-2021
-regression/ecqm-content-qicore-2022
+regression/bundles/*
+regression/default-bundles/*
 data-requirements/fqm-e-dr/*
 data-requirements/jan-2024-connectathon/*
 data-requirements/sept-2023-connectathon/*
diff --git a/regression/bundles/.gitkeep b/regression/bundles/.gitkeep
new file mode 100644
index 00000000..3d81b7ba
--- /dev/null
+++ b/regression/bundles/.gitkeep
@@ -0,0 +1 @@
+# keep this directory
\ No newline at end of file
diff --git a/regression/default-bundles/.gitkeep b/regression/default-bundles/.gitkeep
new file mode 100644
index 00000000..3d81b7ba
--- /dev/null
+++ b/regression/default-bundles/.gitkeep
@@ -0,0 +1 @@
+# keep this directory
\ No newline at end of file
diff --git a/regression/regression.ts b/regression/regression.ts
index 71a6c1c2..3a7edfeb 100644
--- a/regression/regression.ts
+++ b/regression/regression.ts
@@ -4,13 +4,12 @@ import { Calculator } from '../src';
 
 const regressionBaseName = process.argv[2] ?? 'regression-output';
 const verbose = process.argv[3] === 'true';
-const internal = process.argv[4] === 'true';
 
 const REGRESSION_OUTPUT_DIR = path.join(__dirname, `./output/${regressionBaseName}`);
-const CTHON_BASE_PATH = path.join(__dirname, './connectathon/fhir401/bundles/measure');
-const ECQM_CONTENT_BASE_PATH = path.join(__dirname, './ecqm-content-r4-2021/bundles/measure');
-const ECQM_CONTENT_QICORE_BASE_PATH = path.join(__dirname, './ecqm-content-qicore-2022/bundles/measure');
-const COVERAGE_BASE_PATH = path.join(__dirname, './coverage-script-bundles/measure');
+const CTHON_BASE_PATH = path.join(__dirname, './default-bundles/connectathon/fhir401/bundles/measure');
+const ECQM_CONTENT_BASE_PATH = path.join(__dirname, './default-bundles/ecqm-content-r4-2021/bundles/measure');
+const ECQM_CONTENT_QICORE_BASE_PATH = path.join(__dirname, './default-bundles/ecqm-content-qicore-2022/bundles/measure');
+const BUNDLES_BASE_PATH = path.join(__dirname, './bundles'); // folders in this directory are assumed to have a coverage script bundles format
 
 const RESET = '\x1b[0m';
 const FG_YELLOW = '\x1b[33m';
@@ -120,11 +119,14 @@ async function main() {
     await calculateRegression(filesPath, testFilePaths, measureBundle, dir.shortName);
   }
 
-  if (internal) {
+  // Everything in the BUNDLES_BASE_PATH directory is expected in $set_name/measure/$measure_name structure with 
+  // $measure_name-v332.json, $measure_name-v314.json, and $measure_name-TestCases folder within
+  const baseBundlePaths = fs.readdirSync(BUNDLES_BASE_PATH).filter(f => !f.startsWith('.')).map(f => (path.join(BUNDLES_BASE_PATH, f, 'measure')));
+  await baseBundlePaths.forEach( async dirPath => {
     // coverage directory organized with multiple measures for each set of test files
-    const covDirs = fs.readdirSync(COVERAGE_BASE_PATH).map(f => ({
+    const covDirs = fs.readdirSync(dirPath).map(f => ({
       shortName: f,
-      fullPath: path.join(COVERAGE_BASE_PATH, f)
+      fullPath: path.join(dirPath, f)
     }));
     for (const dir of covDirs) {
       const basePath = dir.fullPath;
@@ -147,7 +149,7 @@ async function main() {
       ) as fhir4.Bundle;
       await calculateRegression(patientDirectoryPath, testFilePaths, measureBundle332, `${dir.shortName}-v332`);
     }
-  }
+  });
 }
 
 main().then(() => console.log('done'));
diff --git a/regression/run-regression.sh b/regression/run-regression.sh
index 833498aa..62149ba2 100755
--- a/regression/run-regression.sh
+++ b/regression/run-regression.sh
@@ -10,18 +10,18 @@ GREEN='\033[0;32m'
 NC='\033[0m'
 
 VERBOSE=false
-INTERNAL=false
+PULL_BUNDLES=false
 BASE_BRANCH="master"
 
 function usage() {
     cat <<USAGE
 
-    Usage: $0 [-b|--base-branch <branch-name>] [-v|--verbose] [-i|--internal]
+    Usage: $0 [-b|--base-branch <branch-name>] [-v|--verbose] [-p|--pull-bundles]
 
     Options:
         -b/--base-branch:   Base branch to compare results with (default: master)
         -v/--verbose:       Use verbose regression. Will print out diffs of failing JSON files with spacing (default: false)
-        -i/--internal:      Include limited-access internal resources in the test files (default: false)
+        -p/--pull-bundles:  Pull bundles from default repositories into the default-bundles directory
 USAGE
     exit 1
 }
@@ -30,7 +30,7 @@ while test $# != 0
 do
     case "$1" in
     -v | --verbose) VERBOSE=true ;;
-    -i | --internal) INTERNAL=true ;;
+    -p | --pull-bundles) PULL_BUNDLES=true ;;
     -b | --base-branch)
       shift
       BASE_BRANCH=$1
@@ -40,20 +40,24 @@ do
     shift
 done
 
-if [ ! -d "regression/connectathon" ]; then
-  git clone https://github.com/dbcg/connectathon.git regression/connectathon
-fi
-
-if [ ! -d "regression/ecqm-content-r4-2021" ]; then
-  git clone https://github.com/cqframework/ecqm-content-r4-2021.git regression/ecqm-content-r4-2021
-fi
+if [ $PULL_BUNDLES = "true" ]; then
+  if [ ! -d "regression/default-bundles/connectathon" ]; then
+    git clone https://github.com/dbcg/connectathon.git regression/default-bundles/connectathon
+  else
+    git -C regression/default-bundles/connectathon/ pull origin master
+  fi
 
-if [ ! -d "regression/ecqm-content-qicore-2022" ]; then
-  git clone https://github.com/cqframework/ecqm-content-qicore-2022.git regression/ecqm-content-qicore-2022
-fi
+  if [ ! -d "regression/default-bundles/ecqm-content-r4-2021" ]; then
+    git clone https://github.com/cqframework/ecqm-content-r4-2021.git regression/default-bundles/ecqm-content-r4-2021
+  else
+    git -C regression/default-bundles/ecqm-content-r4-2021/ pull origin master
+  fi
 
-if [ $INTERNAL = "true" ] && [ ! -d "regression/coverage-script-bundles" ]; then
-  git clone https://gitlab.mitre.org/flame/coverage-script-bundles.git regression/coverage-script-bundles
+  if [ ! -d "regression/default-bundles/ecqm-content-qicore-2022" ]; then
+    git clone https://github.com/cqframework/ecqm-content-qicore-2022.git regression/default-bundles/ecqm-content-qicore-2022
+  else
+    git -C regression/default-bundles/ecqm-content-qicore-2022/ pull origin master
+  fi
 fi
 
 git fetch --all
@@ -70,13 +74,13 @@ TIMESTAMP=$(date +%s)
 echo "Gathering results on current branch '$CURRENT_BRANCH'"
 
 npm i
-npx ts-node --files ./regression/regression.ts "$CURRENT_BRANCH-$TIMESTAMP" $VERBOSE $INTERNAL
+npx ts-node --files ./regression/regression.ts "$CURRENT_BRANCH-$TIMESTAMP" $VERBOSE
 
 echo "Gathering results on base branch '$BASE_BRANCH'"
 git checkout $BASE_BRANCH
 
 npm i
-npx ts-node --files ./regression/regression.ts "$BASE_BRANCH-$TIMESTAMP" $VERBOSE $INTERNAL
+npx ts-node --files ./regression/regression.ts "$BASE_BRANCH-$TIMESTAMP" $VERBOSE
 
 FAILURES=()
 BASE_BRANCH_BASE_PATH="regression/output/$BASE_BRANCH-$TIMESTAMP"