I'll start by saying that the GECK is a plot device. A
McGuffin. It had the ability to save Arroyo when in the hands of the Chosen One or a learned member of the wastes.
As a crude plot device, it may also be used as seen fit to create plots and plant new and exciting adventure seeds as needed. As a result, all of the material in this section is subject to change based on the whims of whoever wants to play with the GECK.
If you want it to be a magic box of 1950s science, that's cool - we might do it, too. However, my current take on it is, it's not some miracle device, it's a little more down to earth - more like a deconstruction kit, if you will.
The GECK isn't really a replicator. It contains a fertilizer system, with a variety of food seeds, soil supplements, and chemicals that could fertilize arid wasteland (and possibly selected sections of the moon's surface pre-conditioned to accept the GECK) into supporting farming. The GECK is intended to be "disassembled" over the course of its use to help build communities (for example, the cold fusion power source is intended to be used for main city power production), and so on. Anything else people needed, they could simply consult the How To Books/Library of Congress/Encyclopedias in the GECK
holodisk library for more knowledge. The pen flashlight was just a bonus.
The GECK also contained some basic force field schematics as well as info on how to make adobe-type buildings from the landscape (or contain chemicals that can create "sand-crete" walls).
As for clothing, the GECK contained codes that allowed the Vault to create more varieties of jumpsuits (and weatherproof gear) from their dispensers, which they could do anyway before the GECK. It's possible the GECK contained other codes that could unlock more functionality within the Vault computers that weren't initially available because they would jeopardize the survival of the Vault if they were used or scavenged (or else they would interfere with the
Grand Experiment).
Also, the GECKs also tell the Vault inhabitants how to disassemble sections of their Vault (or take extraneous systems from the Vault) to create new homes and defensive structures on the surface.
The "just add water" comment/joke for the GECK in the description in
Fallout 2 refers to the fact that part of the GECK's operations require that the Vault Dwellers use water from their water purification system in the Vault to help with the agriculture, irrigation, and possibly the cold fusion as well. It wasn't meant literally. If you want it to be, that's cool, too. Go for it.
To close, the "basic replicator" mentioned in the Fallout 1 manual is nothing more than a selection of seeds and fertilizers. The fact that it can "build basic items" is intended to mean that you can use it to help break down sections of the Vault into items usable in a community, as well as provide new codes for the machines in the Vault to create new items from the dispensers and computers.