diff --git a/classes/create_repo.php b/classes/create_repo.php
index 8ca1d8e..6f076c4 100644
--- a/classes/create_repo.php
+++ b/classes/create_repo.php
@@ -84,6 +84,12 @@ class create_repo {
      * @var string
      */
     public string $manifestpath;
+    /**
+     * Path to actual manifest file.
+     *
+     * @var string
+     */
+    public string $nonquizmanifestpath;
     /**
      * Path to temporary manifest file.
      *
@@ -134,6 +140,8 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
         } else {
             $this->directory = $arguments['rootdirectory'];
         }
+        $this->nonquizmanifestpath = ($arguments['rootdirectory']) ?
+                    $arguments['rootdirectory'] . '/' . $arguments['nonquizmanifestpath'] : $arguments['nonquizmanifestpath'];
         $this->subcategory = ($arguments['subcategory']) ? $arguments['subcategory'] : 'top';
         if (is_array($arguments['token'])) {
             $token = $arguments['token'][$moodleinstance];
diff --git a/classes/export_quiz.php b/classes/export_quiz.php
index 2a7b6bc..5885e7e 100644
--- a/classes/export_quiz.php
+++ b/classes/export_quiz.php
@@ -107,6 +107,7 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
         // Convert command line options into variables.
         $arguments = $clihelper->get_arguments();
         $moodleinstance = $arguments['moodleinstance'];
+        $this->moodleurl = $moodleinstances[$moodleinstance];
         $rootdirectory = ($arguments['rootdirectory']) ? $arguments['rootdirectory'] . '/' : '';
         $this->quizmanifestpath = ($arguments['quizmanifestpath']) ?
                     $rootdirectory . $arguments['quizmanifestpath'] : null;
@@ -115,6 +116,10 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             echo "\nUnable to access or parse manifest file: {$this->quizmanifestpath}\nAborting.\n";
             $this->call_exit();
         }
+        if ($this->quizmanifestcontents->context->moodleurl !== $this->moodleurl) {
+            echo "\nManifest file is for the wrong Moodle instance: {$this->quizmanifestpath}\nAborting.\n";
+            $this->call_exit();
+        }
         $instanceid = $this->quizmanifestcontents->context->instanceid;
         if ($arguments['nonquizmanifestpath']) {
             $this->nonquizmanifestpath = ($arguments['nonquizmanifestpath']) ?
@@ -124,6 +129,10 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
                 echo "\nUnable to access or parse manifest file: {$this->nonquizmanifestpath}\nAborting.\n";
                 $this->call_exit();
             }
+            if ($this->nonquizmanifestcontents->context->moodleurl !== $this->moodleurl) {
+                echo "\nManifest file is for the wrong Moodle instance: {$this->nonquizmanifestpath}\nAborting.\n";
+                $this->call_exit();
+            }
         }
         if (is_array($arguments['token'])) {
             $token = $arguments['token'][$moodleinstance];
@@ -131,7 +140,6 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             $token = $arguments['token'];
         }
 
-        $this->moodleurl = $moodleinstances[$moodleinstance];
         $wsurl = $this->moodleurl . '/webservice/rest/server.php';
 
         $this->curlrequest = $this->get_curl_request($wsurl);
diff --git a/classes/export_repo.php b/classes/export_repo.php
index 285aab8..8404ebd 100644
--- a/classes/export_repo.php
+++ b/classes/export_repo.php
@@ -68,6 +68,12 @@ class export_repo {
      * @var string
      */
     public string $manifestpath;
+    /**
+     * Full path to manifest file
+     *
+     * @var string
+     */
+    public string $nonquizmanifestpath;
     /**
      * Path to temporary manifest file
      *
@@ -120,6 +126,8 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
         $defaultwarning = false;
         $this->manifestpath = ($arguments['rootdirectory']) ? $arguments['rootdirectory'] . '/' . $arguments['manifestpath'] :
                                                             $arguments['manifestpath'];
+        $this->nonquizmanifestpath = ($arguments['rootdirectory']) ?
+                    $arguments['rootdirectory'] . '/' . $arguments['nonquizmanifestpath'] : $arguments['nonquizmanifestpath'];
         if (is_array($arguments['token'])) {
             $token = $arguments['token'][$moodleinstance];
         } else {
@@ -130,6 +138,11 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             echo "\nUnable to access or parse manifest file: {$this->manifestpath}\nAborting.\n";
             $this->call_exit();
         }
+        if ($this->manifestcontents->context->moodleurl !== $this->moodleurl) {
+            echo "\nManifest file is for the wrong Moodle instance: {$this->manifestcontents}\nAborting.\n";
+            $this->call_exit();
+        }
+
         if ($arguments['subcategory']) {
             $this->subcategory = $arguments['subcategory'];
             $qcategoryid = null;
@@ -376,21 +389,6 @@ public function call_repo_creation(string $rootdirectory, string $moodleinstance
                 '" -l "module" -n ' . $instanceid . ' -t ' . $token . $ignorecat);
     }
 
-    /**
-     * Separate out exec call for mocking.
-     *
-     * @param string $moodleinstance
-     * @param string $token
-     * @param string $quizmanifestpath
-     * @return string|null
-     */
-    public function call_export_quiz(string $moodleinstance, string $token,
-                                    string $quizmanifestpath, string $scriptdirectory): ?string {
-        chdir($scriptdirectory);
-        return shell_exec('php exportquizstructurefrommoodle.php -u ' . $this->usegit . ' -w -r "" -i "' . $moodleinstance . '" -t '
-                . $token. ' -p "' . $this->manifestpath . '" -f "' . $quizmanifestpath . '"');
-    }
-
     /**
      * Separate out exec call for mocking.
      *
diff --git a/classes/export_trait.php b/classes/export_trait.php
index 1c1cdac..09f3ab2 100644
--- a/classes/export_trait.php
+++ b/classes/export_trait.php
@@ -247,9 +247,10 @@ public function export_quiz_structure($clihelper, $scriptdirectory) {
     public function call_export_quiz(string $moodleinstance, string $token,
                                     string $quizmanifestpath, string $scriptdirectory): ?string {
         chdir($scriptdirectory);
+        $nonquiz = ($this->nonquizmanifestpath) ? ' -p "' . $this->nonquizmanifestpath . '"' : '';
         return shell_exec('php exportquizstructurefrommoodle.php -u ' . $this->usegit .
                 ' -w -r "" -i "' . $moodleinstance . '" -t "'
-                . $token. '" -p "' . $this->manifestpath . '" -f "' . $quizmanifestpath . '"');
+                . $token. '" -f "' . $quizmanifestpath . '"' . $nonquiz);
     }
 
     /**
diff --git a/classes/import_quiz.php b/classes/import_quiz.php
index abfc54d..caec9c8 100644
--- a/classes/import_quiz.php
+++ b/classes/import_quiz.php
@@ -140,6 +140,7 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
         $directoryprefix = ($directory) ? $directory . '/' : '';
         $coursename = $arguments['coursename'];
         $moodleinstance = $arguments['moodleinstance'];
+        $this->moodleurl = $moodleinstances[$moodleinstance];
         $instanceid = $arguments['instanceid'];
         $contextlevel = 50;
         $this->usegit = $arguments['usegit'];
@@ -150,8 +151,11 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             if (!$this->quizmanifestcontents) {
                 echo "\nUnable to access or parse manifest file: {$this->quizmanifestpath}\nAborting.\n";
                 $this->call_exit();
-
             } else {
+                if ($this->quizmanifestcontents->context->moodleurl !== $this->moodleurl) {
+                    echo "\nManifest file is for the wrong Moodle instance: {$this->quizmanifestpath}\nAborting.\n";
+                    $this->call_exit();
+                }
                 $this->cmid = $this->quizmanifestcontents->context->instanceid;
                 $this->quizdatapath = ($arguments['quizdatapath']) ? $directoryprefix . $arguments['quizdatapath']
                                         : cli_helper::get_quiz_structure_path($this->quizmanifestcontents->context->modulename,
@@ -188,13 +192,17 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             }
         }
         if (!empty($arguments['nonquizmanifestpath'])) {
-            $this->nonquizmanifestpath = ($arguments['nonquizmanifestpath']) ?
-                                $directoryprefix . $arguments['nonquizmanifestpath'] : null;
+            $this->nonquizmanifestpath = ($arguments['rootdirectory']) ?
+                    $arguments['rootdirectory'] . '/' . $arguments['nonquizmanifestpath'] : $arguments['nonquizmanifestpath'];
             $this->nonquizmanifestcontents = json_decode(file_get_contents($this->nonquizmanifestpath));
             if (!$this->nonquizmanifestcontents) {
                 echo "\nUnable to access or parse manifest file: {$this->nonquizmanifestpath}\nAborting.\n";
                 $this->call_exit();
             }
+            if ($this->nonquizmanifestcontents->context->moodleurl !== $this->moodleurl) {
+                echo "\nManifest file is for the wrong Moodle instance: {$this->nonquizmanifestpath}\nAborting.\n";
+                $this->call_exit();
+            }
             if (!$instanceid && $this->nonquizmanifestcontents->context->contextlevel === cli_helper::get_context_level('course')) {
                 $instanceid = $this->nonquizmanifestcontents->context->instanceid;
             }
@@ -216,7 +224,6 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             $token = $arguments['token'];
         }
 
-        $this->moodleurl = $moodleinstances[$moodleinstance];
         $wsurl = $this->moodleurl . '/webservice/rest/server.php';
 
         $this->listcurlrequest = $this->get_curl_request($wsurl);
@@ -310,6 +317,8 @@ public function import_all($clihelper, $scriptdirectory): void {
         } else {
             $directory = $arguments['rootdirectory'];
         }
+        $this->nonquizmanifestpath = ($arguments['rootdirectory']) ?
+                $arguments['rootdirectory'] . '/' . $arguments['nonquizmanifestpath'] : $arguments['nonquizmanifestpath'];
         if (is_array($arguments['token'])) {
             $token = $arguments['token'][$moodleinstance];
         } else {
@@ -353,10 +362,10 @@ public function call_import_repo(string $rootdirectory, string $moodleinstance,
      */
     public function call_import_quiz_data(string $moodleinstance, string $token, string $scriptdirectory): ?string {
         chdir($scriptdirectory);
+        $nonquiz = ($this->nonquizmanifestpath) ? ' -p "' . $this->nonquizmanifestpath . '"' : '';
         return shell_exec('php importquizstructuretomoodle.php -u ' . $this->usegit .
-                    ' -w -r "" -i "' . $moodleinstance . '" -t ' . $token. ' -p "' . $this->nonquizmanifestpath.
-                    '" -a "' . $this->quizdatapath .
-                    '" -f "' . $this->quizmanifestpath. '"');
+                    ' -w -r "" -i "' . $moodleinstance . '" -t ' . $token. ' -a "' . $this->quizdatapath .
+                    '" -f "' . $this->quizmanifestpath. '"' . $nonquiz);
     }
 
     /**
diff --git a/classes/import_repo.php b/classes/import_repo.php
index 5deac4b..a4eb167 100644
--- a/classes/import_repo.php
+++ b/classes/import_repo.php
@@ -306,6 +306,10 @@ public function __construct(cli_helper $clihelper, array $moodleinstances) {
             $this->manifestcontents->questions = [];
         } else {
             $this->manifestcontents = $manifestcontents;
+            if ($this->manifestcontents->context->moodleurl !== $this->moodleurl) {
+                echo "\nManifest file is for the wrong Moodle instance: {$this->manifestcontents}\nAborting.\n";
+                $this->call_exit();
+            }
         }
 
         if ($manifestpath) {
@@ -871,7 +875,7 @@ public function check_question_versions(): void {
     }
 
     /**
-     * Create/update quizzes.
+     * Create/update quizzes for whole course.
      * @param object $clihelper
      * @param string $scriptdirectory - directory of CLI scripts
      * @return void
diff --git a/cli/createrepo.php b/cli/createrepo.php
index 888aa76..3d44865 100755
--- a/cli/createrepo.php
+++ b/cli/createrepo.php
@@ -115,6 +115,14 @@
         'variable' => 'instanceid',
         'valuerequired' => true,
     ],
+    [
+        'longopt' => 'nonquizmanifestpath',
+        'shortopt' => 'p',
+        'description' => 'Filepath of non-quiz manifest file relative to root directory.',
+        'default' => null,
+        'variable' => 'nonquizmanifestpath',
+        'valuerequired' => true,
+    ],
     [
         'longopt' => 'token',
         'shortopt' => 't',
@@ -169,12 +177,14 @@
 $createrepo->process();
 $clihelper->commit_hash_setup($createrepo);
 // If we're exporting a quiz then we try getting the structure as well.
-// Skip if we're creating a whole cpurse repo or we'll do it twice!
+// Skip if we're creating a whole course repo or we'll do it twice!
 if ($createrepo->manifestcontents->context->contextlevel === 70 && !$clihelper->get_arguments()['subcall']) {
     $scriptdirectory = dirname(__FILE__);
     $createrepo->export_quiz_structure($clihelper, $scriptdirectory);
-    chdir(dirname($createrepo->manifestpath));
-    exec("git add --all");
-    exec('git commit -m "Initial Commit - Quiz structure"');
+    if ($clihelper->get_arguments()['usegit']) {
+        chdir(dirname($createrepo->manifestpath));
+        exec("git add --all");
+        exec('git commit -m "Initial Commit - Quiz structure"');
+    }
 }
 
diff --git a/cli/exportquizstructurefrommoodle.php b/cli/exportquizstructurefrommoodle.php
index 9a0a210..1fad703 100644
--- a/cli/exportquizstructurefrommoodle.php
+++ b/cli/exportquizstructurefrommoodle.php
@@ -104,12 +104,6 @@
 }
 $clihelper = new cli_helper($options);
 $exportquiz = new export_quiz($clihelper, $moodleinstances);
-if ($exportquiz->nonquizmanifestpath) {
-    if (empty($clihelper->get_arguments()['subcall'])) {
-        echo "Checking repo...\n";
-    }
-    $clihelper->check_for_changes($exportquiz->nonquizmanifestpath);
-}
 if ($exportquiz->quizmanifestpath) {
     if (empty($clihelper->get_arguments()['subcall'])) {
         echo "Checking quiz repo...\n";
diff --git a/cli/exportrepofrommoodle.php b/cli/exportrepofrommoodle.php
index fc4a3a7..d0cedcf 100644
--- a/cli/exportrepofrommoodle.php
+++ b/cli/exportrepofrommoodle.php
@@ -49,6 +49,14 @@
         'variable' => 'rootdirectory',
         'valuerequired' => true,
     ],
+    [
+        'longopt' => 'nonquizmanifestpath',
+        'shortopt' => 'p',
+        'description' => 'Filepath of non-quiz manifest file relative to root directory.',
+        'default' => null,
+        'variable' => 'nonquizmanifestpath',
+        'valuerequired' => true,
+    ],
     [
         'longopt' => 'manifestpath',
         'shortopt' => 'f',
diff --git a/cli/importquizstructuretomoodle.php b/cli/importquizstructuretomoodle.php
index e5d4e39..af38947 100644
--- a/cli/importquizstructuretomoodle.php
+++ b/cli/importquizstructuretomoodle.php
@@ -131,10 +131,6 @@
 
 $clihelper = new cli_helper($options);
 $importquiz = new import_quiz($clihelper, $moodleinstances);
-if ($importquiz->nonquizmanifestpath && empty($clihelper->get_arguments()['subcall'])) {
-    echo "Checking repo...\n";
-    $clihelper->check_for_changes($importquiz->nonquizmanifestpath);
-}
 if ($importquiz->quizmanifestpath && empty($clihelper->get_arguments()['subcall'])) {
     echo "Checking quiz repo...\n";
     $clihelper->check_for_changes($importquiz->quizmanifestpath);
diff --git a/cli/importquiztomoodle.php b/cli/importquiztomoodle.php
index 433f344..1270efc 100755
--- a/cli/importquiztomoodle.php
+++ b/cli/importquiztomoodle.php
@@ -73,6 +73,14 @@
         'valuerequired' => true,
         'hidden' => true,
     ],
+    [
+        'longopt' => 'nonquizmanifestpath',
+        'shortopt' => 'p',
+        'description' => 'Filepath of non-quiz manifest file relative to root directory.',
+        'default' => null,
+        'variable' => 'nonquizmanifestpath',
+        'valuerequired' => true,
+    ],
     [
         'longopt' => 'quizdatapath',
         'shortopt' => 'a',
diff --git a/doc/importquiztomoodle.md b/doc/importquiztomoodle.md
index 32b6816..89effc3 100644
--- a/doc/importquiztomoodle.md
+++ b/doc/importquiztomoodle.md
@@ -20,7 +20,7 @@ Commit this update.
 |-|-|-|
 |i|moodleinstance|Key of Moodle instance in  moodleinstances to use. Should match end of instance URL.|
 |r|rootdirectory|Directory on user's computer containing repos.|
-|f|manifestpath|Filepath of manifest file relative to root directory.|
+|p|nonquizmanifestpath|Filepath of manifest file relative to root directory.|
 |a|quizdatapath|Filepath of quiz data file relative to root directory.
 |d|directory|Directory of repo on users computer containing "top" folder, relative to root directory.|
 |s|subdirectory|Relative subdirectory of repo to actually import.|
diff --git a/doc/usinggit.md b/doc/usinggit.md
index 41152a0..0f8dd78 100644
--- a/doc/usinggit.md
+++ b/doc/usinggit.md
@@ -174,11 +174,11 @@ Import questions again after updates in the repo:
 Create quiz and import into course with `id=2`:  
 `php importquiztomoodle.php -d 'quizexport' -n 2`
 
-### To handle a quiz that only uses questions from another context
-- `createrepo.php` will export the questions into the new repo but will not export the structure and will list the questions from other contexts.
-- `exportrepofrommoodle.php` will update the questions in the repo.
-- Use `exportquizstructurefrommoodle.php` to export the quiz structure from Moodle.
-- Use `importquiztomoodle.php` for initial import of questions and structure into a Moodle instance. (Quiz will be created within a specified course.)
+### To handle a quiz that uses questions from another context
+- `createrepo.php` will export the questions into the new repo but will not export the structure and will list the questions from other contexts unless you also supply a manifest file containing the additional questions.
+- `exportrepofrommoodle.php` will update the questions in the repo (and the quiz structure if you supply the manifest file again).
+- Use `exportquizstructurefrommoodle.php` to export just the quiz structure from Moodle if needed.
+- Use `importquiztomoodle.php` for initial import of questions and structure into a Moodle instance. (The quiz will be created within a specified course.)
 - Use `importrepotomoodle.php` to update questions in Moodle.
 - Manually update structure in Moodle.
 
@@ -186,18 +186,14 @@ Example:
 Initialise repo for quiz:  
 `git init quizexport`  
 Export quiz with `cmid=50` into directory `quizexport` (assuming rootdirectory, token, moodleinstance, usegit, etc, all set in your config file.):  
-`php createrepo.php -d 'quizexport' -l module -n 50`  
-Export quiz structure by supplying quiz and course manifests:  
-`php exportquizstructurefrommoodle.php -f 'quizexport/instance1_module_course-1_mixed-quiz_question_manifest.json' -p 'course1/instance1_course_course-1_question_manifest.json'`  
+`php createrepo.php -d 'quizexport' -l module -n 49 -p 'course1/instance1_course_course-1_question_manifest.json'`  
 Export questions/structures again after updates in Moodle:  
-`php exportrepofrommoodle.php -f 'quizexport/instance1_module_course-1_quiz-only_question_manifest.json'`  
-`php exportquizstructurefrommoodle.php -f 'quizexport/instance1_module_course-1_mixed-quiz_question_manifest.json' -p 'course1/instance1_course_course-1_question_manifest.json'`  
+`php exportrepofrommoodle.php -f 'quizexport/instance1_module_course-1_mixed-quiz_question_manifest.json' -p 'course1/instance1_course_course-1_question_manifest.json'`  
 Import questions again after updates in the repo:  
-`php importrepotomoodle.php -f 'quizexport/instance1_module_course-1_quiz-only_question_manifest.json'`  
+`php importrepotomoodle.php -f 'quizexport/instance1_module_course-1_mixed-quiz_question_manifest.json'`  
 Create quiz and import into course with `id=2`:  
 `php importquiztomoodle.php -d 'quizexport' -n 2 -p 'course1/instance1_course_course-1_question_manifest.json'`  
 
-
 ### To handle a course and its quizzes in a single repo
 - `createwholecourserepo.php` will export a course context and associated quizzes in sibling directories. As long as the quizzes only use questions from the course and their own context, the quiz structures will be exported.
 - `exportwholecoursefrommoodle.php` will update the questions and quiz structures in the repo.