One thing I'll point out now is that not every app requires this type of set up. But this is the most generic set up and shouldn't cause problems for those apps that don't require it. It will just make things a bit more messy for you.
@Andrew, I think this might be a good sticky candidate.
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1. Create a portable directory for your app. From here on "your app" will be referred to as %appname%. So if your app is generally known as Snafu, then replace %appname% with Snafu everywhere within this document. - Don't create the directory on the desktop or in Program Files or MyDocuments, etc. - Use some place like "E:\Portables\%appname%". From here on this directory will be referred to as %appdir%. 2. Copy JPE's distributed JauntePE_jauntePE.ini file to %appdir%. 3. Edit it to contain the additional following lines at the top (sans numbering): 1. [Registry] 2. Use=1 3. Data=.\jauntePE_registry.reg 4. 5. [Filesystem] 6. Use=1 7. Data=.\ 8. 9. [Redirection] 10. Logging=1 4. Copy the %appname% installer to %appdir%. If it doesn't have one, then do the following: - Create a "Files" sub-directory in %appdir%. - Create a "ProgramFiles" sub-directory in "Files". - Create a %appname% sub-directory in "ProgramFiles". - Copy all of the app's files and sub-directories to this lowest-level sub- directory, i.e., copy to %appdir%\Files\ProgramFiles\%appname%. - Skip to step 8. 5. Start JPE and drag-n-drop the %appname% installer onto the JPE launchpad. 6. Open up the launchpad icon's properties and: - Check "Registry", - Check "File system", - Check "App-specific registry storage", - Un-check "In-memory registry". 7. Run the %appname% installer via the JPE launchpad icon: - Accept the settings per your requirements, but make sure that the app is to be installed in the typical "%ProgramFiles%\%appname%" location, where %ProgramFiles% is the full path to your standard "Program Files" directory. - Don't have it run the app or do anything else after the installation has completed. 8. Create a JauntePE_jauntePE.ini in the %appdir%\Files\ProgramFiles\%appname% directory that contains the following lines (sans numbering): 1. [Registry] 2. Use=1 3. Ini=..\..\..\JauntePE_jauntePE.ini 4. 5. [Filesystem] 6. Use=1 7. Ini=..\..\..\JauntePE_jauntePE.ini 9. Drag-n-drop the %appdir%\Files\ProgramFiles\%appname%\%appname%.exe file onto the JPE launchpad. 10. Open up the launchpad icon's properties and: - Check "Registry", - Check "File system", - Check "App-specific registry storage", - Un-check "In-memory registry". 11. Run the %appname% app via the JPE launchpad icon. 12. If all goes well, then you can, if you wish, modify the %appdir% directory's JauntePE_jauntePE.ini file to be more specific to your app, i.e., optimize the redirection entries to create the fastest possible JPEized solution, use the build wizard to create a standalone app launcher for it, etc. I like to keep the launchpad icons handy for editing, re-building, etc. If the new JPE gui is ever released, it allows you to edit the app-specific JPE runtime settings just like you can now edit the default equivalents.