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Pathologic was missing because of a .git folder inside.
[yaffs-website]
/
web
/
modules
/
contrib
/
pathologic
/
src
/
Tests
/
drwxr-xr-x
..
-rw-r--r--
11502
PathologicTest.php
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-rw-r--r--
3418
PathologicUITest.php
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projects / yaffs-website / tree