// The problemic directory in this example is modules/taxonomy. Specifically /var/www/docroot/modules/taxonomy.

// Here I list the parent directory 'modules', as you can see taxonomy/ is not listed:

vagrant@nexus7ad:/var/www/docroot$ ls -al modules/
total 4
drwxr-xr-x 43 501 dialout 1376 Jul  6 17:51 .
drwxr-xr-x 27 501 dialout  864 Dec  5 23:43 ..
...
drwxr-xr-x 36 501 dialout 1152 Dec  5 23:43 system
drwxr-xr-x  9 501 dialout  288 Dec  5 23:43 toolbar
drwxr-xr-x  8 501 dialout  256 Dec  5 23:43 tracker
drwxr-xr-x  7 501 dialout  224 Dec  5 23:43 translation
drwxr-xr-x  9 501 dialout  288 Dec  5 23:43 trigger
drwxr-xr-x 16 501 dialout  512 Dec  5 23:43 update
...

// Here I list the taxonomy directory that didn't appear before and you can see that the directory exists and has contents.

vagrant@nexus7ad:/var/www/docroot$ ls -al modules/taxonomy/
total 264
drwxr-xr-x 13 501 dialout   416 Dec  5 23:43 .
drwxr-xr-x 43 501 dialout  1376 Jul  6 17:51 ..
-rw-r--r--  1 501 dialout 36578 Jul  6 17:51 taxonomy.admin.inc
-rw-r--r--  1 501 dialout  6052 Jul  6 17:51 taxonomy.api.php
-rw-r--r--  1 501 dialout   232 Jul  6 17:51 taxonomy.css
-rw-r--r--  1 501 dialout   353 Dec  5 23:43 taxonomy.info
-rw-r--r--  1 501 dialout 30893 Dec  5 23:43 taxonomy.install
-rw-r--r--  1 501 dialout  1770 Jul  6 17:51 taxonomy.js
-rw-r--r--  1 501 dialout 71738 Dec  5 23:43 taxonomy.module
-rw-r--r--  1 501 dialout  6713 Dec  5 23:43 taxonomy.pages.inc
-rw-r--r--  1 501 dialout  2144 Jul  6 17:51 taxonomy-term.tpl.php
-rw-r--r--  1 501 dialout 83367 Dec  5 23:43 taxonomy.test
-rw-r--r--  1 501 dialout  6028 Jul  6 17:51 taxonomy.tokens.inc