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When I ssh into my phone via SSHDroid, it sets me at the following path by default.

/data/data/berserker.android.apps.sshdroid/home/

I can use cd to maneuver around but it causes problems when I try to use scp because files are obviously not stored in this directory. It there anyway to change this setting?

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try pushd and popd, [not exactly an answer to your settings question but, it might work] assuming you have root privilege.

Okay for this example i am starting in /storage/extSdCard and need to copy target tass.txt from /sdcard/tess

extSdCard # HERE=$PWD                                                                                                                                                                                                 
extSdCard # echo $HERE                                                                                                                                                                                                
/storage/extSdCard
extSdCard # pushd /sdcard/tess                                                                                                                                                                                        
~/tess /storage/extSdCard
tess # pwd                                                                                                                                                                                                            
/sdcard/tess
tess # ls $PWD                                                                                                                                                                                                        
tass.txt
tess # cp * $HERE                                                                                                                                                                                                     
tess # popd                                                                          
/storage/extSdCard
extSdCard # ls tass.txt
tass.txt
extSdCard # popd                                                                          
tmp-mksh: popd: directory stack empty
extSdCard #  
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