Terminal not showing invisible files/system files

Question

My terminal application has stopped showing system files files
eg:
Macbook:~ julianmerrow-smith$ ls -l
total 32
drwx------+ 21 julianmerrow-smith staff 714 Oct 20 11:46 Desktop
drwx------+ 5 julianmerrow-smith staff 170 Oct 20 11:46 Documents
drwx------+ 61 julianmerrow-smith staff 2074 Oct 20 08:06 Downloads
drwx------+ 39 julianmerrow-smith staff 1326 Oct 19 20:45 Library
drwx------+ 3 julianmerrow-smith staff 102 Sep 27 11:37 Movies
drwx------+ 3 julianmerrow-smith staff 102 Sep 27 11:37 Music
drwx------+ 5 julianmerrow-smith staff 170 Sep 27 21:09 Pictures
drwxr-xr-x+ 5 julianmerrow-smith staff 170 Sep 27 11:37 Public
drwxr-xr-x+ 5 julianmerrow-smith staff 170 Sep 27 11:37 Sites
-rw-r--r-- 1 julianmerrow-smith staff 800 Oct 7 12:15 artforsale.pwm
-rw-r--r-- 1 julianmerrow-smith staff 800 Oct 7 12:15 artforsale.pwm_bak1
drwxr-xr-x@ 33 julianmerrow-smith staff 1122 Sep 27 14:35 be2bqu21.default
-rw-r--r-- 1 julianmerrow-smith staff 744 Sep 28 09:02 mt-config.cgi
drwxr-xr-x 3 julianmerrow-smith staff 102 Oct 20 10:30 server back-ups
-rw-r--r--@ 1 julianmerrow-smith staff 2668 Oct 20 09:07 untitled.html
I created a new admin, same result. sudo bash has given me back use of the terminal but how do I get it back to normal, any ideas?

Answer 1

There are two kinds of "invisible" files and folders - those items whose names begin with a period, and those items which carry a "hidden" flag. Both are normally invisible to Finder, though Finder can be enabled to see them both. Terminal's ls command requires the -a option in order to see items with names that begin with a period, but does not need the -a option to see items that carry the "hidden" flag.
Are you looking for something specific? You listed the contents of your home folder, which doesn't normally contain any executable system files, and doesn't normally contain any items which are invisible because of the "hidden" flag. The home folder does contain a few items with names beginning with a period, which you would be able to see if you use *ls -la*. Of these, the .Trash folder is probably the only item that is of practical interest.
There are invisible system files and folders at the root level of your startup volume. If you want to see all of these, you can use
ls -la /
Even without the -a option, the command
ls -l /
will show those hidden system items that are of most practical interest (/Volumes, /bin, /etc, /private, /sbin, /tmp, /usr, /var )