This is not the only way to get FreeDOS tools working, but I found it the most elegant. It took me some time to figure this out, so I made this guide in the hope it may be useful to others.

This process allows you to use the FDIMPLES package manager to install and remove FreeDOS packages directly from within the DOSBox environment.

1. Set up the following environment variables; you may adjust the paths to your liking.
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   1REM The main directory for FreeDOS utilities:
   2SET DOSDIR=C:\FDOS
   3REM A temporary directory used to kickstart the installation process
   4SET TEMP=C:\TEMP
   5SET FDNPKG.CFG=%TEMP%\FDNPKG.CFG
   

2. Extract the following files from the FreeDOS CD into the %TEMP% directory:
   • FD13LIVE.ISO\packages\util\fdnpkg.zip\BIN\FDNPKG.EXE
   • FD13LIVE.ISO\packages\util\fdnpkg.zip\BIN\FDNPKG.CFG
   How exactly you extract these files is up to you, but it may be easiest to do it from outside DOSBox. If you have an UNZIP utility of some kind already installed, you may use that from within DOSBox after mounting FD13LIVE.ISO. In any case, the key is to get those two listed files into %TEMP%.
3. Mount FD13LIVE.ISO within DOSBox (if you haven't yet). You can use any available drive letter.
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   1IMGMOUNT E /data/images/FD13LIVE.ISO -t cdrom
   

4. Use (the temporary) FDNPKG to properly install itself into %DOSDIR%.
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   1C:\TEMP\FDNPKG.EXE INSTALL E:\PACKAGES\UTIL\FDNPKG.ZIP
   

   Adjust paths as necessary. Note that you cannot use the %TEMP% variable directly on the command line (it only works in batch files); you must invoke the entire path literally.
5. After the installation completes successfully, remove the temp files and unset the CFG variable. It may confuse FDIMPLES if you keep it set, so this step should be considered mandatory.
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   1DEL C:\TEMP\*.*
   2SET FDNPKG.CFG=
   

6. Install FDIMPLES using (the now properly-installed) FDNPKG:
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   1C:\FDOS\BIN\FDNPKG.EXE INSTALL E:\PACKAGES\APPS\FDIMPLES.ZIP
   

7. If there were no errors up to this point, you're done! You can invoke FDIMPLES, which is now correctly installed:
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   1C:\FDOS\BIN\FDIMPLES.EXE
   

   If the FD13LIVE.ISO image is still mounted, FDIMPLES will recognize it and provide you with a list of packages to install. Notably FDNPKG and FDIMPLES itself will be shown as already installed.
   You can swap the mounted image for FD13BNS.ISO to install the Bonus packages also.

This process results in a clean installation of FDIMPLES which can manage all FreeDOS packages from this point on. In the future, you only need to mount the appropriate FreeDOS ISO image and have the %DOSDIR% variable set. FDIMPLES will "just work".