Using the complete file list you made, make sure file and folder permissions are what they should be. Although your complete file list is a text file, the search isn't too difficult. You can search for suspicious "world-writable" 777 folder permissions by searching for the equivalent "rwxrwxrwx" in the text. World-writable 666 file permissions appear in the text as "rw-rw-rw-".
Common correct permissions for world-readable (but not world-writable) folders are 755 (rwxr-xr-x), and common permissions for world-readable files are 644 (rw-r--r--). Those are what you should mostly expect to see.
There are only two situations where world needs write access (777 / 666), and both only apply if your server is configured with PHP as an Apache module:
* A file needs 666 permissions if PHP needs to a) open the file and write data into it, or b) copy another file to the directory entry currently occupied by this file.
* A folder needs 777 permissions if PHP needs to a) dynamically create new files in it, or b) delete existing files from it. However, if PHP only needs to open and modify the contents of an existing file or even copy another file to the directory slot occupied by an existing file, the folder does not need 777 permissions. It is only necessary that the destination file have 666 permissions. That is counterintuitive because you would think that copying a file involves deleting the existing file and putting the new file where it was, but that is not how Linux views it. It only considers it a change in the file's content, not a change to the directory, so the directory can remain read-only. This is important because there may be some files that PHP only needs to create once, during a program's initial installation when it's setting up its data files. After that, it's possible PHP can do everything it needs with the file set to 666 but the directory locked back down to read-only 755. That is much better because although that one file remains potentially vulnerable to modification, a hacker cannot put new malicious files in a 755 directory.
If you find world-writable permissions on a file or folder, consider it potentially suspicious because those are areas the hacker could have accessed most easily:
1. Check the contents of 777 folders to ensure they don't contain malicious new files.
2. Check the contents of 666 files to ensure they don't contain new malicious code.
3. If you can't think of a good reason why the loose permissions are necessary (does PHP really need to make the changes those permissions allow?), try tightening them to 755 / 644.
4. Even if you do know why the loose permissions are necessary, try to think of a way to make those permissions unnecessary.