I have a .bat file on my Windows machine. This .bat file uses plink.exe to connect to an Ubuntu machine and execute an .sh
I had to hack a solution to work around this problem. Adding a "-i" option at the header of the bash script I was invoking from my .bat file did the trick:
#!/bin/bash -i
Note some warn of unwanted side effects (no mention of specifics tho...) when using this option. But calling this now interactive script from a remote ssh session (e.g. when using plink.exe from a Windows .bat file and passing inline commands to the Unix box) solves any issues regarding file/directory visibility & permission issues.
Note to plink users: if you're calling a script on Unix via plink and noticing that the script doesn't behave as expected...adding the "-i" may help debug/solve your problem. Again, note that some have claimed unwanted side-effects of this hack of which they/I'm unaware.