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Gerber import is not straightforward since Gerber files are not necessarily self-contained entities. You'll need a little background knowledge for that.
Did you have a look at http://klayout.de/doc/manual/import_gerber.html yet? I hope it's comprehensive.
A Gerber file does not make much sense as a single entity. A "project" describes a PCB board. A board will almost always consist of multiple files - artwork, drill files and maybe others. Hence, to import PCB data to a multilayer flow, it's not sufficient to just take some file and import it somehow. Typically the files do not have a certain extension too. ".gbr" is not a common choice - you'll find every kind of extensions is a typical PCB project. So there is no way to bind the format to a specific extension.
As the name says, the functionality is to "import" a PCB layout. In order to provide the necessary side information, at little work cannot be avoided. That specifically applies to the mapping of drill files to the usual VLSI interconnect concept. Coated drill holes may connect multiple routing layers while via holes just connect two.
If you just want to view files, you should look for gerbv which is an excellent alternative. KLayout's function was supplied to connect GDS layouts with PCB data and that is a different scope.
The base directory feature is intentional - it will always be the location of the import.pcb file. If you want to supply paths relative to he import.pcb file, specify "workdir/filename.gbr" for your individual files. You can also use absolute paths for single files, but that way you won't be able to easily move a PCB project somewhere else or archive it.
Maybe I was not explicit enough: if you're seriously looking into Gerber, there is gerbv and many other tools. KLayout is a silicon layout tool and there are multiple layers, a particular idea of connectivity, few round features and not much use for apertures and so on. Gerber support was specifically designed to import of PCB data into the IC world. You're looking at a special functionality here.
You can still import single files, but that's a special case only. It's possible to automate single Gerber file import somewhat by scripting the generation of an import.pcb file - it's a tiny piece of XML file and KLayout will recognize it as a layout format of it's own. In that sense, import.pcb provides the metadata required.
Regarding the file extension I definitly disagree - regardless of what Wikipedia says. I got a lot of samples out of different systems. Plus I studied a lot of PCB data available to the public, for example for demo board layouts. Here is a brief selection of extensions: .art, .drl, .gbl, .tx1, .tx2, .tx3, .g1, .g2, .g3, .g4, .gtl, .exc, .bot, .bsk, .bsm, .bsy, .gnd, .vdd, .tsk, .p01, .p02, .p03, .p04, .pcb and even without extension ... there are some .gbr too, but there's not a clear preference.
And regarding the "base directory" - it's supposed to be used initially. When you start a new project and you set up a base directory, the file names are stored relative to that path. If not, the file names will be stored as absolute paths. If you use a base path and save the .pcb file into the directory (Disclaimer - it's right, it does not go there by default), then the files are in the proper place and can be found relative to the .pcb.
I would like to import Gerber files in batch mode. I found that you mentioned to "import.pcb" file. Could you show how to build this file?