[CentOS] explain strange behavior

Fri Aug 19 18:12:57 UTC 2016
Dan Hyatt <dhyatt at dsgmail.wustl.edu>

In my bin directory, most of the binaries are linked to it. It is in my 
path. I have googled this and cannot find anything close.

I am running bash on centos6.8

When I run   "which command" most of the files in this custom bin 
directory show up.

When I run "which file.jar" it cannot see it, but I can *ls* the file  
(soft link)

as which only works on executables (according to man page), I created a 
dan.jar empty file and did a which on dan.tar and found it.

can anyone explain what is happening and how I can soft link the jar 
files to my bin directory so which can see them?