Having an issue getting coverage for mapping

global class Clarke_AttachmentTriggerHandler {
    
    Map<Id, List<ContentDocumentLink>> linkMap = new Map<Id, List<ContentDocumentLink>>();
    Map<String, Directory__c> directoryMap = new Map<String, Directory__c>();
    List<ContentDocumentLink> cdl_List = new List<ContentDocumentLink>();
    public ContentDocumentLink cdl = New ContentDocumentLink();

    global override void bulkBeforeExtended() {
        if( Trigger.isUpdate ){
            List<Id> docIds = new List<Id>();
            List<String> parentIds = new List<String>();
            List<String> categoryvals = new List<String>();

            for( Attachment__c record : ( List<Attachment__c> ) Trigger.new ){
                Id docId = record.ContentDocumentId__c;
                    String parentId = record.Parent_ID__c ;
                    Id recId = Id.valueOf(record.Parent_ID__c ); 
                    String parentObjectType = String.valueOf( recId.getSObjectType() );
                    if( parentObjectType == 'Activity__c' ){
                        parentId = record.Proj__c;
                    }
                    if( docId != null ){    
                        docIds.add( docId );
                    }
                    if( parentId != null ){    
                        parentIds.add( parentId );
                    }    
            }

            list<Directory__c> dirs = [
                SELECT id,Directory_Template__c,Name,ParentId__c,Sobject__c,
                    (Select Id,Name, Directory__c, Folder_Template__c,Parent_File_Folder__c FROM File_Folders__r ORDER BY Name)
                FROM Directory__c 
                WHERE ParentId__c IN: parentIds
            ];

            if( !dirs.isEmpty() ){
                for( Directory__c dir : dirs ){
                    this.directoryMap.put( dir.ParentId__c, dir );
                }
            }

            List<ContentDocumentLink> linkList = [ SELECT Id, ContentDocumentId, LinkedEntityId FROM ContentDocumentLink WHERE ContentDocumentId IN: docIds ];
            if( !linkList.isEmpty() ){
                for( ContentDocumentLink link : linkList ){
                    List<ContentDocumentLink> links = this.linkMap.containsKey( link.ContentDocumentId )
                        ? this.linkMap.get( link.ContentDocumentId ) : new List<ContentDocumentLink>();
                    links.add( link );
                    this.linkMap.put( link.ContentDocumentId, links );
                }
            }
        }
    }
    global override void bulkAfterExtended() {}

    global override void beforeInsertExtended(SObject so) {
       Attachment__c newAttachment = ( Attachment__c ) so;

        if( this.linkMap.containsKey( newAttachment.ContentDocumentId__c ) ){
            List<ContentDocumentLink> links = this.linkMap.get( newAttachment.ContentDocumentId__c );
            if( !links.isEmpty() ){
                for( ContentDocumentLink link : links ){
                    String objectType = String.valueOf( link.LinkedEntityId.getSObjectType() );
                    Directory__c dir = this.directoryMap.containsKey( link.LinkedEntityId )
                        ? this.directoryMap.get( link.LinkedEntityId ) : null;
                    if( dir != null ){
                        switch on ( objectType ){
                            when 'Site__c' {
                                newAttachment.Site__c = link.LinkedEntityId;
                            }
                            when 'Programme__c' {
                                newAttachment.Programme__c = link.LinkedEntityId;
                            }
                            when 'Activity__c' {
                               newAttachment.Activity__c= link.LinkedEntityId;
                            }
                            when 'Project__c' {
                                newAttachment.Proj__c = link.LinkedEntityId;
                            }
                        }
                    }
                }
            }
        }
    }
    global override void beforeUpdateExtended(SObject oldso, SObject newso) {
        Attachment__c newAttachment = ( Attachment__c ) newSo;
        String folderparentId = newAttachment.Parent_Id__c;
        Id recId = Id.valueOf(newAttachment.Parent_ID__c );
        String parentObjectType = String.valueOf( recId.getSObjectType() );

        if( parentObjectType == 'Activity__c' ){
            folderparentId = newAttachment.Proj__c;
        }

        if( directoryMap.containsKey( folderparentId)){           
            Directory__c dir = this.directoryMap.get( folderparentId );
            List<File_Folder__c> folders = dir.File_Folders__r;
            List<ContentDocumentLink> links = this.linkMap.get( newAttachment.ContentDocumentId__c );

            for (ContentDocumentLink cont : links ){
                for (File_Folder__c folder: folders ){
                    if(newattachment.Document_Type__c == folder.name ){
                        ContentDocumentLink cdl = new ContentDocumentLink();
                        cdl.LinkedEntityId = folder.Id;
                        cdl.ContentDocumentId = cont.ContentDocumentId;
                        cdl.ShareType = 'V';
                        cdl.Visibility = 'AllUsers';

                        newAttachment.File_Folder__c = folder.Id;
                        cdl_List.add(cdl);
                        break;
                    }
                }
            }
        }
    }
    global override void afterUpdateExtended(SObject oldso, SObject newso) {}
    global override void afterInsertExtended(SObject newso) {} 
    global override void andFinallyExtended() {
    
      if (!Trigger.isDelete) {
            if (Trigger.isUpdate) {
                try {
                    if (cdl_List.size() > 0) {
                        insert cdl_List;
                    }
                } catch (Exception e) {
                    System.debug('Error: ' + e.getMessage());
                }
            }
        }
    }
}

Test Class

@isTest
private class Clarke_AttachmentTriggerHandlerTest {
     @TestSetup
    static void CreateTestData() {
        
        Site__c site = new Site__c(Name = 'Test Site');
        insert site;

        System.assert(site.Id != null);

        Project_Template__c newTemplate = new Project_Template__c(
            Name = 'test template'
        );
        insert newTemplate;

        Project__c proj = new Project__c(
           Site__c = site.id
          
        );
        insert proj;

        Activity__c activity = new Activity__c(
            Project__c = proj.Id
        );
        insert activity;

        Programme__c programme = new Programme__c(Name = 'Test Program');
        insert programme;

        List<Attachment__c> attachments = new List<Attachment__c>{
            new Attachment__c(Parent_ID__c = site.Id),
            new Attachment__c(Parent_ID__c = proj.Id),
            new Attachment__c(Parent_ID__c = programme.Id),
            new Attachment__c()
        };
        insert attachments;

        attachments = [SELECT Id,Document_Type__c,Name FROM Attachment__c WHERE Site__r.Name = 'Test Site'];
        System.assertEquals(1, attachments.size(), 'Site attachment records');
        
         Directory_Template__c dt = new Directory_Template__c(
            Name = 'Test Directory Template'
        );
        insert dt;

        //dt.Active__c = true;
        //update dt;

        File_Folder_Template__c ft = new File_Folder_Template__c(
            Name = 'Test Folder Template',
            Directory_Template__c = dt.Id
        );
        insert ft;

        File_Folder_Template__c ftc = new File_Folder_Template__c(
            Name = 'Test Folder Template Child',
            Directory_Template__c = dt.Id,
            Parent_Folder_Template__c = ft.id
        );
        insert ftc; 
    }
    
    @isTest
    private static void TestFunction(){
    
     Test.startTest();
     List<Project_Template__c> templates = [
              SELECT Id FROM Project_Template__c
                ];
    
      List<Site__c> sites = [SELECT Id FROM Site__c];
                System.assertEquals( 1, sites.size(), '1 site found' );
                
            Project__c proj = new Project__c(
           Site__c =  sites[ 0 ].Id
           
        );
        insert proj;

        ContentVersion ContentDoc = new ContentVersion();
        ContentDoc.Title = 'Test Title';
        ContentDoc.ContentUrl= 'test.com';
        Insert ContentDoc;
    
            ContentVersion contentVersion = new ContentVersion(
                    Title          = 'a picture',
                    PathOnClient   = 'Pic.jpg',
                    VersionData    = Blob.valueOf('Test Content'),
                    IsMajorVersion = true);
            insert contentVersion;

            List<ContentDocument> documents = [SELECT Id, Title, LatestPublishedVersionId FROM ContentDocument];

            ContentDocumentLink cdl = new ContentDocumentLink();
            cdl.LinkedEntityId = proj.Id;
            cdl.ContentDocumentId = documents[0].Id;
            cdl.ShareType = 'V';
            cdl.Visibility = 'AllUsers';
            insert cdl;
            
            List<ContentDocument> cdList = [SELECT Id, Title, LatestPublishedVersionId FROM ContentDocument];
            List<ContentDocumentLink> files=[SELECT Id, ContentDocumentId, ContentDocument.LatestPublishedVersionId, LinkedEntityId, ContentDocument.Title 
                                         from ContentDocumentLink where ContentDocumentId =: documents[0].Id]; 
     Test.stopTest();

    }
}

I am having an issue with the mapping/containsKey
Never goes past:

if( this.linkMap.containsKey( newAttachment.ContentDocumentId__c ) ){

or 

if( directoryMap.containsKey( folderparentId)){

Any suggestion is appreciated.
Thanks 
P