Hrm, something somewhere has gone wrong, and was exposed by my upgrade from 2.0 to 3.0 alpha 11.

Code:
empeg:/empeg# ls -al
total 4
drwxr-xr-x    4 0        0            1024 Jul 25  2005 .
drwxr-xr-x   15 521      220          1024 Oct  6 01:45 ..
drwxr-xr-x    2 0        0            1024 Jul 25  2005 bin
lrwxrwxrwx    1 0        220            14 Jul 25  2005 fids0 -> ../drive0/fids
lrwxrwxrwx    1 0        220            14 Jul 25  2005 fids1 -> ../drive1/fids
drwxr-xr-x    6 0        0            1024 Jul 25  2005 lib
lrwxrwxrwx    1 0        220            13 Jul 25  2005 var -> ../drive0/var
empeg:/empeg# ls -al /drive0
total 2
drwxr-xr-x    2 0        0            1024 Jul  6  1999 .
drwxr-xr-x   15 521      220          1024 Oct  6 01:45 ..
empeg:/empeg# ls -al /drive1
total 2
drwxr-xr-x    2 0        0            1024 Jun  2  1999 .
drwxr-xr-x   15 521      220          1024 Oct  6 01:45 ..
empeg:/empeg# mount
/dev/root on / type ext2 (rw)
none on /proc type proc (rw)
empeg:/empeg# fdisk -l /dev/hda

Disk /dev/hda: 255 heads, 63 sectors, 3899 cylinders
Units = cylinders of 16065 * 512 bytes

   Device Boot    Start       End    Blocks   Id  System
/dev/hda1             1         5     40131    5  Extended
/dev/hda2             6        10     40162+  83  Linux
/dev/hda3            11        13     24097+  10  OPUS
/dev/hda4            14      3899  31214295   83  Linux
/dev/hda5             1         3     24034+  83  Linux
/dev/hda6             4         5     16033+  82  Linux swap
empeg:/empeg# fdisk -l /dev/hdc

Disk /dev/hdc: 255 heads, 63 sectors, 3899 cylinders
Units = cylinders of 16065 * 512 bytes

   Device Boot    Start       End    Blocks   Id  System
/dev/hdc1             1         5     33232+   5  Extended
Partition 1 does not end on cylinder boundary:
     phys=(65, 15, 63) should be (65, 254, 63)
/dev/hdc2             5         9     33264   83  Linux
Partition 2 does not end on cylinder boundary:
     phys=(131, 15, 63) should be (131, 254, 63)
/dev/hdc3             9        11     16632   10  OPUS
Partition 3 does not end on cylinder boundary:
     phys=(164, 15, 63) should be (164, 254, 63)
/dev/hdc4            11      3900  31242960   83  Linux
Partition 4 does not end on cylinder boundary:
     phys=(1023, 15, 63) should be (1023, 254, 63)
/dev/hdc5             1         3     16569   83  Linux
/dev/hdc6             3         5     16600+  82  Linux swap


For the drive expansion, I ended up using gparted with the CF cards attached to a USB to IDE adaptor. /dev/hda is the CF card I cloned in the empeg first. /dev/hdc was cloned on my Mac using dd. I think my attempt to hang onto the nostalgia of all my old music loadout, along with whatever crazy hacks* I was doing in the past, and the HDD->CF conversion has introduced so many variables. Time I think to just nuke it from orbit and move forward with the new plans to integrate it into my newer music strategy.

* I was finding remnants of the GPS app, empire, emphatic, various web interfaces, my old distributed.net setup, strongbad TTS clock, random bits of debian linux, and some other things still on the drives.