diff --git a/bin/process_all.sh b/bin/process_all.sh
index 34fbb48..84a23c4 100644
--- a/bin/process_all.sh
+++ b/bin/process_all.sh
@@ -85,9 +85,11 @@ mkdir -p "${BASEPATH}/users"
 
     ############################################################################
     # Run Lichen
-    ./tokenize_all.py    "$tmp_location" || { rm -rf "$tmp_location"; exit 1; }
-    ./hash_all.py        "$tmp_location" || { rm -rf "$tmp_location"; exit 1; }
-    ./compare_hashes.out "$tmp_location" || { rm -rf "$tmp_location"; echo "${KILL_ERROR_MESSAGE}"; exit 1; }
+    {  # We still want to unzip files if an error occurs when running Lichen here
+      ./tokenize_all.py    "$tmp_location" &&
+      ./hash_all.py        "$tmp_location" &&
+      ./compare_hashes.out "$tmp_location" || echo "${KILL_ERROR_MESSAGE}";
+    }
 
     ############################################################################
     # Zip the results back up and send them back to the course's lichen directory
diff --git a/compare_hashes/compare_hashes.cpp b/compare_hashes/compare_hashes.cpp
index 91eeab5..ed7d4d0 100644
--- a/compare_hashes/compare_hashes.cpp
+++ b/compare_hashes/compare_hashes.cpp
@@ -157,8 +157,8 @@ int main(int argc, char* argv[]) {
   std::unordered_set<hash> provided_code;
   // stores all hashes from other gradeables
   std::unordered_map<hash, std::unordered_map<user_id, std::vector<HashLocation>>> other_gradeables;
-  // stores the highest match for every student, used later for generating overall_rankings.txt
-  std::unordered_map<user_id, std::pair<int, Score>> highest_matches;
+  // stores the matches for every student, used later for generating overall_rankings.txt
+  std::unordered_map<user_id, std::vector<std::pair<version_number, Score>>> highest_matches;
   // keeps track of max matching hashes across all submissions, used for calculation of ranking score
   unsigned int max_hashes_matched = 0;
 
@@ -283,7 +283,7 @@ int main(int argc, char* argv[]) {
         }
       }
 
-      // if the hash doesn't match any of the provided code's hashes, try to find matched between other students
+      // if the hash doesn't match any of the provided code's hashes, try to find matches between other students
       if (!provided_match_found) {
         // look up that hash in the all_hashes table, loop over all other students that have the same hash
         std::unordered_map<std::string, std::vector<HashLocation>> occurences = all_hashes[hash_itr->first];
@@ -333,23 +333,6 @@ int main(int argc, char* argv[]) {
       continue;
     }
 
-    // Save this submissions highest percent match for later when we generate overall_rankings.txt
-    float percentMatch = (*submission_itr)->getPercentage();
-    unsigned int totalMatchingHashes = (*submission_itr)->getMatchCount();
-    Score submission_score(totalMatchingHashes, percentMatch);
-    if (max_hashes_matched < totalMatchingHashes) {
-      max_hashes_matched = totalMatchingHashes;
-    }
-
-    std::unordered_map<user_id, std::pair<int, Score> >::iterator highest_matches_itr = highest_matches.find((*submission_itr)->student());
-    std::pair<int, Score> new_pair = {(*submission_itr)->version(), submission_score};
-    if (highest_matches_itr == highest_matches.end()) {
-      highest_matches.insert({(*submission_itr)->student(), new_pair});
-    }
-    else if (submission_score > highest_matches_itr->second.second) {
-      highest_matches_itr->second = new_pair;
-    }
-
     // =========================================================================
     // Write matches.json file
 
@@ -563,6 +546,19 @@ int main(int argc, char* argv[]) {
       }
     }
 
+    // =========================================================================
+    // Save this submission's highest percent match for later when we generate overall_rankings.txt
+    float percentMatch = (*submission_itr)->getPercentage();
+    unsigned int totalMatchingHashes = (*submission_itr)->getMatchCount();
+    Score submission_score(totalMatchingHashes, percentMatch);
+    if (max_hashes_matched < totalMatchingHashes) {
+      max_hashes_matched = totalMatchingHashes;
+    }
+    
+    std::pair<version_number, Score> new_pair = {(*submission_itr)->version(), submission_score};
+    highest_matches[(*submission_itr)->student()].push_back(new_pair);
+    // =========================================================================
+
     std::sort(student_ranking.begin(), student_ranking.end(), ranking_sorter);
 
     // create the directory and a file to write into
@@ -609,10 +605,18 @@ int main(int argc, char* argv[]) {
   // take the map of highest matches and convert it to a vector so we can sort it
   // by percent match and then save it to a file
   std::vector<StudentRanking> ranking;
-  for (std::unordered_map<user_id, std::pair<int, Score> >::iterator itr
+  for (std::unordered_map<user_id, std::vector<std::pair<version_number, Score>>>::iterator itr
         = highest_matches.begin(); itr != highest_matches.end(); ++itr) {
-    ranking.push_back(StudentRanking(itr->first, itr->second.first, "", itr->second.second));
-    ranking[ranking.size()-1].score.calculateScore(max_hashes_matched);
+
+    std::pair<version_number, Score> best_score = itr->second.front();
+    best_score.second.calculateScore(max_hashes_matched);
+    for (unsigned int i=0; i < itr->second.size(); i++) {
+      itr->second[i].second.calculateScore(max_hashes_matched);
+      if (itr->second[i].second > best_score.second) {
+        best_score = itr->second[i];
+      }
+    }
+    ranking.push_back(StudentRanking(itr->first, best_score.first, "", best_score.second));
   }
 
   std::sort(ranking.begin(), ranking.end(), ranking_sorter);
diff --git a/compare_hashes/score.h b/compare_hashes/score.h
index cc44450..af085ed 100644
--- a/compare_hashes/score.h
+++ b/compare_hashes/score.h
@@ -2,6 +2,7 @@
 #define SCORE_H
 
 #include <cassert>
+#include <string>
 
 typedef int location_in_submission;
 typedef unsigned int hash;
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/config.json b/tests/data/test_lichen/multiple_versions/expected_output/config.json
new file mode 100644
index 0000000..9687866
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/config.json
@@ -0,0 +1,18 @@
+{
+    "semester": "f21",
+    "course": "plagiarism",
+    "gradeable": "multiple_versions",
+    "config_id": 1,
+    "version": "all_versions",
+    "regex": [
+        ""
+    ],
+    "regex_dirs": [
+        "submissions"
+    ],
+    "language": "plaintext",
+    "threshold": 10,
+    "hash_size": 4,
+    "other_gradeables": [],
+    "ignore_submissions": []
+}
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/logs/lichen_job_output.txt b/tests/data/test_lichen/multiple_versions/expected_output/logs/lichen_job_output.txt
new file mode 100644
index 0000000..363466d
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/logs/lichen_job_output.txt
@@ -0,0 +1,10 @@
+Beginning Lichen run: 2021-12-21 17:20:31
+CONCATENATE ALL...done in 0 seconds, 949 Bytes concatenated
+TOKENIZE ALL...done in 0 seconds
+HASH ALL...done in 0 seconds
+COMPARE HASHES...finished loading in 0 seconds
+hash walk: 33% complete
+hash walk: 66% complete
+hash walk: 100% complete
+finished walking in 0 seconds
+COMPARE HASHES done in 0 seconds
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/other_gradeables/git_placeholder.txt b/tests/data/test_lichen/multiple_versions/expected_output/other_gradeables/git_placeholder.txt
new file mode 100644
index 0000000..e69de29
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/overall_ranking.txt b/tests/data/test_lichen/multiple_versions/expected_output/overall_ranking.txt
new file mode 100644
index 0000000..76bf21e
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/overall_ranking.txt
@@ -0,0 +1,2 @@
+aphacker              2    81.4%      35
+bitdiddle             1    81.4%      35
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/provided_code/files/git_placeholder.txt b/tests/data/test_lichen/multiple_versions/expected_output/provided_code/files/git_placeholder.txt
new file mode 100644
index 0000000..e69de29
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/provided_code/hashes.txt b/tests/data/test_lichen/multiple_versions/expected_output/provided_code/hashes.txt
new file mode 100644
index 0000000..e69de29
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/provided_code/submission.concatenated b/tests/data/test_lichen/multiple_versions/expected_output/provided_code/submission.concatenated
new file mode 100644
index 0000000..e69de29
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/provided_code/tokens.json b/tests/data/test_lichen/multiple_versions/expected_output/provided_code/tokens.json
new file mode 100644
index 0000000..fe51488
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/provided_code/tokens.json
@@ -0,0 +1 @@
+[]
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/hashes.txt b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/hashes.txt
new file mode 100644
index 0000000..750fd88
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/hashes.txt
@@ -0,0 +1,62 @@
+ccbfc51b
+46d2e902
+0a1bc040
+6d14f9b3
+a5d513dd
+5e030a24
+c715d526
+fd3fa0fe
+b1917b6c
+ccbfc51b
+fcf8964c
+6afa4117
+25a42a47
+2ac066f5
+c6097572
+6011cbf5
+adefe73d
+36182b9f
+36d719a0
+fe129c06
+e44ef48d
+6bb90c04
+083a9efd
+93d49734
+0f905a05
+8bfb058d
+06410254
+61b171ee
+6c920afa
+05660ab4
+30a548ac
+b38f50f3
+2997d7c5
+297c601f
+e8ccd482
+ae6d442f
+4de258e3
+fae8aa98
+24ac3d5d
+fbdad65f
+fc98ba6b
+44bbaa49
+83df01b7
+964fade5
+2ea0ba40
+5494f32a
+e248b1d9
+528feb65
+27d1db1f
+c552988d
+cf65191e
+eff2064e
+0847585b
+c64da9e5
+7b3dc1c1
+045fe7d1
+50ac87da
+f5f088e7
+ecb2eef0
+7d75f52c
+8576ec09
+497a431b
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/matches.json b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/matches.json
new file mode 100644
index 0000000..f88e5d3
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/matches.json
@@ -0,0 +1,136 @@
+[
+    {
+        "end": 4,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 1,
+        "type": "match"
+    },
+    {
+        "end": 6,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 6,
+                        "start": 2
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 2,
+        "type": "match"
+    },
+    {
+        "end": 12,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 12,
+                        "start": 8
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 8,
+        "type": "match"
+    },
+    {
+        "end": 13,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 10,
+        "type": "match"
+    },
+    {
+        "end": 14,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 14,
+                        "start": 11
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 11,
+        "type": "match"
+    },
+    {
+        "end": 20,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 32,
+                        "start": 26
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 14,
+        "type": "match"
+    },
+    {
+        "end": 34,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 46,
+                        "start": 34
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 22,
+        "type": "match"
+    }
+]
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/ranking.txt b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/ranking.txt
new file mode 100644
index 0000000..f2807a3
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/ranking.txt
@@ -0,0 +1 @@
+bitdiddle        1    f21__plagiarism__multiple_versions   32.79%
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/submission.concatenated b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/submission.concatenated
new file mode 100644
index 0000000..dc777e0
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/submission.concatenated
@@ -0,0 +1,2 @@
+==== submission_1.txt ====
+This file is meant to represent the first submission of three in a small test involving users with multiple submissions.  This submission is a little longer than the other two submissions because we want to test that the system still works when the highest matching version is the second version.
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/tokens.json b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/tokens.json
new file mode 100644
index 0000000..88b44e4
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/1/tokens.json
@@ -0,0 +1,392 @@
+[
+    {
+        "char": 1,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 2,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 3,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 4,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 6,
+        "line": 1,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 16,
+        "line": 1,
+        "type": "punctuation",
+        "value": "_"
+    },
+    {
+        "char": 17,
+        "line": 1,
+        "type": "number",
+        "value": 1
+    },
+    {
+        "char": 18,
+        "line": 1,
+        "type": "punctuation",
+        "value": "."
+    },
+    {
+        "char": 19,
+        "line": 1,
+        "type": "string",
+        "value": "txt"
+    },
+    {
+        "char": 23,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 24,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 25,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 26,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 1,
+        "line": 2,
+        "type": "string",
+        "value": "This"
+    },
+    {
+        "char": 6,
+        "line": 2,
+        "type": "string",
+        "value": "file"
+    },
+    {
+        "char": 11,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 14,
+        "line": 2,
+        "type": "string",
+        "value": "meant"
+    },
+    {
+        "char": 20,
+        "line": 2,
+        "type": "string",
+        "value": "to"
+    },
+    {
+        "char": 23,
+        "line": 2,
+        "type": "string",
+        "value": "represent"
+    },
+    {
+        "char": 33,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 37,
+        "line": 2,
+        "type": "string",
+        "value": "first"
+    },
+    {
+        "char": 43,
+        "line": 2,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 54,
+        "line": 2,
+        "type": "string",
+        "value": "of"
+    },
+    {
+        "char": 57,
+        "line": 2,
+        "type": "string",
+        "value": "three"
+    },
+    {
+        "char": 63,
+        "line": 2,
+        "type": "string",
+        "value": "in"
+    },
+    {
+        "char": 66,
+        "line": 2,
+        "type": "string",
+        "value": "a"
+    },
+    {
+        "char": 68,
+        "line": 2,
+        "type": "string",
+        "value": "small"
+    },
+    {
+        "char": 74,
+        "line": 2,
+        "type": "string",
+        "value": "test"
+    },
+    {
+        "char": 79,
+        "line": 2,
+        "type": "string",
+        "value": "involving"
+    },
+    {
+        "char": 89,
+        "line": 2,
+        "type": "string",
+        "value": "users"
+    },
+    {
+        "char": 95,
+        "line": 2,
+        "type": "string",
+        "value": "with"
+    },
+    {
+        "char": 100,
+        "line": 2,
+        "type": "string",
+        "value": "multiple"
+    },
+    {
+        "char": 109,
+        "line": 2,
+        "type": "string",
+        "value": "submissions"
+    },
+    {
+        "char": 120,
+        "line": 2,
+        "type": "punctuation",
+        "value": "."
+    },
+    {
+        "char": 123,
+        "line": 2,
+        "type": "string",
+        "value": "This"
+    },
+    {
+        "char": 128,
+        "line": 2,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 139,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 142,
+        "line": 2,
+        "type": "string",
+        "value": "a"
+    },
+    {
+        "char": 144,
+        "line": 2,
+        "type": "string",
+        "value": "little"
+    },
+    {
+        "char": 151,
+        "line": 2,
+        "type": "string",
+        "value": "longer"
+    },
+    {
+        "char": 158,
+        "line": 2,
+        "type": "string",
+        "value": "than"
+    },
+    {
+        "char": 163,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 167,
+        "line": 2,
+        "type": "string",
+        "value": "other"
+    },
+    {
+        "char": 173,
+        "line": 2,
+        "type": "string",
+        "value": "two"
+    },
+    {
+        "char": 177,
+        "line": 2,
+        "type": "string",
+        "value": "submissions"
+    },
+    {
+        "char": 189,
+        "line": 2,
+        "type": "string",
+        "value": "because"
+    },
+    {
+        "char": 197,
+        "line": 2,
+        "type": "string",
+        "value": "we"
+    },
+    {
+        "char": 200,
+        "line": 2,
+        "type": "string",
+        "value": "want"
+    },
+    {
+        "char": 205,
+        "line": 2,
+        "type": "string",
+        "value": "to"
+    },
+    {
+        "char": 208,
+        "line": 2,
+        "type": "string",
+        "value": "test"
+    },
+    {
+        "char": 213,
+        "line": 2,
+        "type": "string",
+        "value": "that"
+    },
+    {
+        "char": 218,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 222,
+        "line": 2,
+        "type": "string",
+        "value": "system"
+    },
+    {
+        "char": 229,
+        "line": 2,
+        "type": "string",
+        "value": "still"
+    },
+    {
+        "char": 235,
+        "line": 2,
+        "type": "string",
+        "value": "works"
+    },
+    {
+        "char": 241,
+        "line": 2,
+        "type": "string",
+        "value": "when"
+    },
+    {
+        "char": 246,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 250,
+        "line": 2,
+        "type": "string",
+        "value": "highest"
+    },
+    {
+        "char": 258,
+        "line": 2,
+        "type": "string",
+        "value": "matching"
+    },
+    {
+        "char": 267,
+        "line": 2,
+        "type": "string",
+        "value": "version"
+    },
+    {
+        "char": 275,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 278,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 282,
+        "line": 2,
+        "type": "string",
+        "value": "second"
+    },
+    {
+        "char": 289,
+        "line": 2,
+        "type": "string",
+        "value": "version"
+    },
+    {
+        "char": 296,
+        "line": 2,
+        "type": "punctuation",
+        "value": "."
+    }
+]
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/hashes.txt b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/hashes.txt
new file mode 100644
index 0000000..99d4526
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/hashes.txt
@@ -0,0 +1,43 @@
+ccbfc51b
+46d2e902
+0a1bc040
+b8cd789e
+50fb6242
+2ddc3046
+9343e0c2
+fd3fa0fe
+b1917b6c
+ccbfc51b
+fcf8964c
+4c7b788b
+3c78a77e
+0480aa34
+76b55240
+d9fa30ce
+e7e56e4a
+122d719c
+e5056ce3
+9b510320
+134f15c7
+09af10f8
+2ae680fc
+12fbeaef
+9e2a0ae6
+2ac066f5
+c6097572
+6011cbf5
+adefe73d
+bdadb582
+88c09423
+916c300e
+44f252c0
+6bb90c04
+083a9efd
+93d49734
+0f905a05
+8bfb058d
+06410254
+61b171ee
+6c920afa
+05660ab4
+30a548ac
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/matches.json b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/matches.json
new file mode 100644
index 0000000..6f55541
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/matches.json
@@ -0,0 +1,118 @@
+[
+    {
+        "end": 4,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 1,
+        "type": "match"
+    },
+    {
+        "end": 6,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 6,
+                        "start": 2
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 2,
+        "type": "match"
+    },
+    {
+        "end": 12,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 12,
+                        "start": 8
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 8,
+        "type": "match"
+    },
+    {
+        "end": 13,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 10,
+        "type": "match"
+    },
+    {
+        "end": 32,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 32,
+                        "start": 11
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 11,
+        "type": "match"
+    },
+    {
+        "end": 46,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 46,
+                        "start": 34
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "bitdiddle",
+                "version": 1
+            }
+        ],
+        "start": 34,
+        "type": "match"
+    }
+]
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/ranking.txt b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/ranking.txt
new file mode 100644
index 0000000..ceaae6b
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/ranking.txt
@@ -0,0 +1 @@
+bitdiddle        1    f21__plagiarism__multiple_versions   80.95%
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/submission.concatenated b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/submission.concatenated
new file mode 100644
index 0000000..6ffb4eb
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/submission.concatenated
@@ -0,0 +1,2 @@
+==== submission_2.txt ====
+This is a test file for the Lichen plagiarism detection system.  This file is meant to represent the second submission of three in a small test involving users with multiple submissions. 
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/tokens.json b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/tokens.json
new file mode 100644
index 0000000..25e88bc
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/aphacker/2/tokens.json
@@ -0,0 +1,278 @@
+[
+    {
+        "char": 1,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 2,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 3,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 4,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 6,
+        "line": 1,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 16,
+        "line": 1,
+        "type": "punctuation",
+        "value": "_"
+    },
+    {
+        "char": 17,
+        "line": 1,
+        "type": "number",
+        "value": 2
+    },
+    {
+        "char": 18,
+        "line": 1,
+        "type": "punctuation",
+        "value": "."
+    },
+    {
+        "char": 19,
+        "line": 1,
+        "type": "string",
+        "value": "txt"
+    },
+    {
+        "char": 23,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 24,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 25,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 26,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 1,
+        "line": 2,
+        "type": "string",
+        "value": "This"
+    },
+    {
+        "char": 6,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 9,
+        "line": 2,
+        "type": "string",
+        "value": "a"
+    },
+    {
+        "char": 11,
+        "line": 2,
+        "type": "string",
+        "value": "test"
+    },
+    {
+        "char": 16,
+        "line": 2,
+        "type": "string",
+        "value": "file"
+    },
+    {
+        "char": 21,
+        "line": 2,
+        "type": "string",
+        "value": "for"
+    },
+    {
+        "char": 25,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 29,
+        "line": 2,
+        "type": "string",
+        "value": "Lichen"
+    },
+    {
+        "char": 36,
+        "line": 2,
+        "type": "string",
+        "value": "plagiarism"
+    },
+    {
+        "char": 47,
+        "line": 2,
+        "type": "string",
+        "value": "detection"
+    },
+    {
+        "char": 57,
+        "line": 2,
+        "type": "string",
+        "value": "system"
+    },
+    {
+        "char": 63,
+        "line": 2,
+        "type": "punctuation",
+        "value": "."
+    },
+    {
+        "char": 66,
+        "line": 2,
+        "type": "string",
+        "value": "This"
+    },
+    {
+        "char": 71,
+        "line": 2,
+        "type": "string",
+        "value": "file"
+    },
+    {
+        "char": 76,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 79,
+        "line": 2,
+        "type": "string",
+        "value": "meant"
+    },
+    {
+        "char": 85,
+        "line": 2,
+        "type": "string",
+        "value": "to"
+    },
+    {
+        "char": 88,
+        "line": 2,
+        "type": "string",
+        "value": "represent"
+    },
+    {
+        "char": 98,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 102,
+        "line": 2,
+        "type": "string",
+        "value": "second"
+    },
+    {
+        "char": 109,
+        "line": 2,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 120,
+        "line": 2,
+        "type": "string",
+        "value": "of"
+    },
+    {
+        "char": 123,
+        "line": 2,
+        "type": "string",
+        "value": "three"
+    },
+    {
+        "char": 129,
+        "line": 2,
+        "type": "string",
+        "value": "in"
+    },
+    {
+        "char": 132,
+        "line": 2,
+        "type": "string",
+        "value": "a"
+    },
+    {
+        "char": 134,
+        "line": 2,
+        "type": "string",
+        "value": "small"
+    },
+    {
+        "char": 140,
+        "line": 2,
+        "type": "string",
+        "value": "test"
+    },
+    {
+        "char": 145,
+        "line": 2,
+        "type": "string",
+        "value": "involving"
+    },
+    {
+        "char": 155,
+        "line": 2,
+        "type": "string",
+        "value": "users"
+    },
+    {
+        "char": 161,
+        "line": 2,
+        "type": "string",
+        "value": "with"
+    },
+    {
+        "char": 166,
+        "line": 2,
+        "type": "string",
+        "value": "multiple"
+    },
+    {
+        "char": 175,
+        "line": 2,
+        "type": "string",
+        "value": "submissions"
+    },
+    {
+        "char": 186,
+        "line": 2,
+        "type": "punctuation",
+        "value": "."
+    }
+]
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/hashes.txt b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/hashes.txt
new file mode 100644
index 0000000..9d7b5c3
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/hashes.txt
@@ -0,0 +1,43 @@
+ccbfc51b
+46d2e902
+0a1bc040
+b37a3b73
+17f0039d
+ca413f89
+5c7d0821
+fd3fa0fe
+b1917b6c
+ccbfc51b
+fcf8964c
+4c7b788b
+3c78a77e
+0480aa34
+76b55240
+d9fa30ce
+e7e56e4a
+122d719c
+e5056ce3
+9b510320
+134f15c7
+09af10f8
+2ae680fc
+12fbeaef
+9e2a0ae6
+2ac066f5
+c6097572
+6011cbf5
+adefe73d
+6d1d0ed1
+b718f1ae
+bb067147
+7303ecef
+6bb90c04
+083a9efd
+93d49734
+0f905a05
+8bfb058d
+06410254
+61b171ee
+6c920afa
+05660ab4
+30a548ac
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/matches.json b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/matches.json
new file mode 100644
index 0000000..6ab9251
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/matches.json
@@ -0,0 +1,239 @@
+[
+    {
+        "end": 4,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 1,
+        "type": "match"
+    },
+    {
+        "end": 6,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 6,
+                        "start": 2
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 6,
+                        "start": 2
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 2,
+        "type": "match"
+    },
+    {
+        "end": 12,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 12,
+                        "start": 8
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 12,
+                        "start": 8
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 8,
+        "type": "match"
+    },
+    {
+        "end": 13,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 4,
+                        "start": 1
+                    },
+                    {
+                        "end": 13,
+                        "start": 10
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 10,
+        "type": "match"
+    },
+    {
+        "end": 14,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 14,
+                        "start": 11
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 14,
+                        "start": 11
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 11,
+        "type": "match"
+    },
+    {
+        "end": 28,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 28,
+                        "start": 12
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 12,
+        "type": "match"
+    },
+    {
+        "end": 32,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 20,
+                        "start": 14
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 32,
+                        "start": 26
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 26,
+        "type": "match"
+    },
+    {
+        "end": 46,
+        "others": [
+            {
+                "matchingpositions": [
+                    {
+                        "end": 34,
+                        "start": 22
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 1
+            },
+            {
+                "matchingpositions": [
+                    {
+                        "end": 46,
+                        "start": 34
+                    }
+                ],
+                "source_gradeable": "f21__plagiarism__multiple_versions",
+                "username": "aphacker",
+                "version": 2
+            }
+        ],
+        "start": 34,
+        "type": "match"
+    }
+]
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/ranking.txt b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/ranking.txt
new file mode 100644
index 0000000..8f2a405
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/ranking.txt
@@ -0,0 +1,2 @@
+aphacker         2    f21__plagiarism__multiple_versions   80.95%
+aphacker         1    f21__plagiarism__multiple_versions   47.62%
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/submission.concatenated b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/submission.concatenated
new file mode 100644
index 0000000..0e371d1
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/submission.concatenated
@@ -0,0 +1,2 @@
+==== submission_3.txt ====
+This is a test file for the Lichen plagiarism detection system.  This file is meant to represent the third submission of three in a small test involving users with multiple submissions. 
diff --git a/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/tokens.json b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/tokens.json
new file mode 100644
index 0000000..2a2989e
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/expected_output/users/bitdiddle/1/tokens.json
@@ -0,0 +1,278 @@
+[
+    {
+        "char": 1,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 2,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 3,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 4,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 6,
+        "line": 1,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 16,
+        "line": 1,
+        "type": "punctuation",
+        "value": "_"
+    },
+    {
+        "char": 17,
+        "line": 1,
+        "type": "number",
+        "value": 3
+    },
+    {
+        "char": 18,
+        "line": 1,
+        "type": "punctuation",
+        "value": "."
+    },
+    {
+        "char": 19,
+        "line": 1,
+        "type": "string",
+        "value": "txt"
+    },
+    {
+        "char": 23,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 24,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 25,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 26,
+        "line": 1,
+        "type": "punctuation",
+        "value": "="
+    },
+    {
+        "char": 1,
+        "line": 2,
+        "type": "string",
+        "value": "This"
+    },
+    {
+        "char": 6,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 9,
+        "line": 2,
+        "type": "string",
+        "value": "a"
+    },
+    {
+        "char": 11,
+        "line": 2,
+        "type": "string",
+        "value": "test"
+    },
+    {
+        "char": 16,
+        "line": 2,
+        "type": "string",
+        "value": "file"
+    },
+    {
+        "char": 21,
+        "line": 2,
+        "type": "string",
+        "value": "for"
+    },
+    {
+        "char": 25,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 29,
+        "line": 2,
+        "type": "string",
+        "value": "Lichen"
+    },
+    {
+        "char": 36,
+        "line": 2,
+        "type": "string",
+        "value": "plagiarism"
+    },
+    {
+        "char": 47,
+        "line": 2,
+        "type": "string",
+        "value": "detection"
+    },
+    {
+        "char": 57,
+        "line": 2,
+        "type": "string",
+        "value": "system"
+    },
+    {
+        "char": 63,
+        "line": 2,
+        "type": "punctuation",
+        "value": "."
+    },
+    {
+        "char": 66,
+        "line": 2,
+        "type": "string",
+        "value": "This"
+    },
+    {
+        "char": 71,
+        "line": 2,
+        "type": "string",
+        "value": "file"
+    },
+    {
+        "char": 76,
+        "line": 2,
+        "type": "string",
+        "value": "is"
+    },
+    {
+        "char": 79,
+        "line": 2,
+        "type": "string",
+        "value": "meant"
+    },
+    {
+        "char": 85,
+        "line": 2,
+        "type": "string",
+        "value": "to"
+    },
+    {
+        "char": 88,
+        "line": 2,
+        "type": "string",
+        "value": "represent"
+    },
+    {
+        "char": 98,
+        "line": 2,
+        "type": "string",
+        "value": "the"
+    },
+    {
+        "char": 102,
+        "line": 2,
+        "type": "string",
+        "value": "third"
+    },
+    {
+        "char": 108,
+        "line": 2,
+        "type": "string",
+        "value": "submission"
+    },
+    {
+        "char": 119,
+        "line": 2,
+        "type": "string",
+        "value": "of"
+    },
+    {
+        "char": 122,
+        "line": 2,
+        "type": "string",
+        "value": "three"
+    },
+    {
+        "char": 128,
+        "line": 2,
+        "type": "string",
+        "value": "in"
+    },
+    {
+        "char": 131,
+        "line": 2,
+        "type": "string",
+        "value": "a"
+    },
+    {
+        "char": 133,
+        "line": 2,
+        "type": "string",
+        "value": "small"
+    },
+    {
+        "char": 139,
+        "line": 2,
+        "type": "string",
+        "value": "test"
+    },
+    {
+        "char": 144,
+        "line": 2,
+        "type": "string",
+        "value": "involving"
+    },
+    {
+        "char": 154,
+        "line": 2,
+        "type": "string",
+        "value": "users"
+    },
+    {
+        "char": 160,
+        "line": 2,
+        "type": "string",
+        "value": "with"
+    },
+    {
+        "char": 165,
+        "line": 2,
+        "type": "string",
+        "value": "multiple"
+    },
+    {
+        "char": 174,
+        "line": 2,
+        "type": "string",
+        "value": "submissions"
+    },
+    {
+        "char": 185,
+        "line": 2,
+        "type": "punctuation",
+        "value": "."
+    }
+]
diff --git a/tests/data/test_lichen/multiple_versions/input/config.json b/tests/data/test_lichen/multiple_versions/input/config.json
new file mode 100644
index 0000000..9687866
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/input/config.json
@@ -0,0 +1,18 @@
+{
+    "semester": "f21",
+    "course": "plagiarism",
+    "gradeable": "multiple_versions",
+    "config_id": 1,
+    "version": "all_versions",
+    "regex": [
+        ""
+    ],
+    "regex_dirs": [
+        "submissions"
+    ],
+    "language": "plaintext",
+    "threshold": 10,
+    "hash_size": 4,
+    "other_gradeables": [],
+    "ignore_submissions": []
+}
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/aphacker/1/submission_1.txt b/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/aphacker/1/submission_1.txt
new file mode 100644
index 0000000..8e0cb11
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/aphacker/1/submission_1.txt
@@ -0,0 +1 @@
+This file is meant to represent the first submission of three in a small test involving users with multiple submissions.  This submission is a little longer than the other two submissions because we want to test that the system still works when the highest matching version is the second version.
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/aphacker/2/submission_2.txt b/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/aphacker/2/submission_2.txt
new file mode 100644
index 0000000..ec9cee0
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/aphacker/2/submission_2.txt
@@ -0,0 +1 @@
+This is a test file for the Lichen plagiarism detection system.  This file is meant to represent the second submission of three in a small test involving users with multiple submissions. 
\ No newline at end of file
diff --git a/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/bitdiddle/1/submission_3.txt b/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/bitdiddle/1/submission_3.txt
new file mode 100644
index 0000000..6569e28
--- /dev/null
+++ b/tests/data/test_lichen/multiple_versions/input/f21/plagiarism/submissions/multiple_versions/bitdiddle/1/submission_3.txt
@@ -0,0 +1 @@
+This is a test file for the Lichen plagiarism detection system.  This file is meant to represent the third submission of three in a small test involving users with multiple submissions. 
\ No newline at end of file
diff --git a/tests/integration/test.py b/tests/integration/test.py
index 810294f..b974596 100644
--- a/tests/integration/test.py
+++ b/tests/integration/test.py
@@ -21,26 +21,35 @@ def testLichen(self):
                 data_path = Path(test_data_dir, "test_lichen", test_case, "input")
                 shutil.copyfile(Path(data_path, "config.json"), Path(temp_dir, "config.json"))
 
+                # change the group for the temporary directory such that it matches the input group
+                subprocess.check_call(f"chgrp -R {data_path.group()} {temp_dir}", shell=True)
+
                 # run Lichen
                 subprocess.check_call(f"bash {str(lichen_installation_dir)}/bin/process_all.sh {str(temp_dir)} {str(data_path)}", shell=True)
 
                 ex_output_path = Path(test_data_dir, "test_lichen", test_case, "expected_output")
 
                 # compare the output and expected output directory structure and file contents
+                ignored_files_count = 0
                 ex_files_count = 0
                 for root, dirs, files in os.walk(ex_output_path):
                     ex_files_count += len(dirs) + len(files)
                     for file in files:
-                        if file != "lichen_job_output.txt" and file != "git_placeholder.txt":
-                            ex_path = Path(root, file)
-                            if root.replace(str(ex_output_path), "") == "":
-                                act_path = Path(temp_dir, file)
-                            else:
-                                act_path = Path(temp_dir, root.replace(str(ex_output_path), "").strip("/"), file)
+                        if file == "lichen_job_output.txt":
+                            continue
+                        if file == "git_placeholder.txt":
+                            ignored_files_count += 1
+                            continue
+
+                        ex_path = Path(root, file)
+                        if root.replace(str(ex_output_path), "") == "":
+                            act_path = Path(temp_dir, file)
+                        else:
+                            act_path = Path(temp_dir, root.replace(str(ex_output_path), "").strip("/"), file)
 
-                            with open(ex_path) as ex_file:
-                                with open(act_path) as act_file:
-                                    self.assertEqual(ex_file.read().strip(), act_file.read().strip())
+                        with open(ex_path) as ex_file:
+                            with open(act_path) as act_file:
+                                self.assertEqual(ex_file.read().strip(), act_file.read().strip())
 
                     for dir in dirs:
                         ex_path = Path(root, dir)
@@ -52,10 +61,8 @@ def testLichen(self):
                         self.assertTrue(os.path.isdir(act_path))
 
                 act_files_count = 0
-                for _, dirs, files in os.walk(temp_dir):
+                for _, dirs, files in os.walk(Path(temp_dir)):
                     act_files_count += len(dirs) + len(files)
 
-                # NOTE: We must subtract two here because git doesn't store empty directories
-                # This will have to change in the future when we add more test gradeables
-                # may not have empty directories
-                self.assertEqual(ex_files_count - 2, act_files_count)
+                # ensure that we didn't miss any files by checking that there are the same number of files in each directory
+                self.assertEqual(ex_files_count - ignored_files_count, act_files_count)