EDIT: Here's my full script and hopefully a better way of explaining what I need done:
#Import
import arcpy, sys, os
# Set environment settings
arcpy.env.workspace = sys.argv[1]
inFiles = sys.argv[2]
outWorkspace = sys.argv[3]
projectGDB = sys.argv[4]+".gdb"
coordinate = sys.argv[5]
clipBoundary = sys.argv[6]
scratchGDB = sys.argv[7]+".gdb"
# CREATE A GEODATABASE
arcpy.CreateFileGDB_management(outWorkspace, projectGDB) # Here I create the database
# for the projected files to go into
arcpy.CreateFileGDB_management(outWorkspace, scratchGDB)
# CHANGE THE PROJECTION
arcpy.BatchProject_management(inFiles, outWorkspace+"\\"+gdbName, coordinate)
# CLIP FEATURES TO STUDY AREA BUFFER
fcs = arcpy.ListFeatureClasses() # Here I need it to somehow read from the GDB with
# my projected files in it that was created above..however it reads from the workspace
# and because the workspace is set before running the script I can not choose the GDB
# because it is not created yet
for fc in fcs:
arcpy.Clip_analysis(fc, clipBoundary, outWorkspace+"\\"+scratchGDB+"\\"+fc+"__clipped")
I am wondering if there is a way to change the workspace as you move through the python script without having to do something like wrap tkinter around it.
For example:
I have set up my inital workspace through the parameters (sys.argv) so that I can create a gdb to store my files - this is a general "Project" folder as my workspace
Next I have a batch project in which the files that the user wants to be projected are chosen, the output of these projected files is to the geodatabse that was created
NEXT (and here's where my issue comes in) I need to clip my projected features to a boundary of the study area, so I have a batch clip written out:
fcs = arcpy.ListFeatureClasses()
for fc in fcs:
arcpy.Clip_analysis(fc, clipBoundary, outWorkspace+"\\"+gdbName+"\\"+fc+"__clipped")
However to select the fc from fcs I need it to be looking into the projected files GDB to read all the feature classes...however if I just run the script from the beginning to this point the workspace is still sitting in my main project folder and therefore there are no feature classes that will be read into the script........

arcpy.env.workspace = sys.argv[1]from line 7 to line 20, after the GDBs are created. – matt wilkie♦ Apr 12 '12 at 19:40