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XBfe (X Bitmap Font Editor) allows you to hand-edit a bitmap font--both the shapes (i.e., the pixels) and the metric information (set widths, side bearings, and kerning tables).
The input is both a bitmap (GF or PK) font and a corresponding TFM file. If you have only a bitmap font for some reason, you can make a TFM file with Fontconvert (see section 8.1.1 Fontconvert output options). XBfe outputs (at your command) the edited files in the current directory with the same name, thus possibly replacing the input file.
XBfe is intended to edit existing fonts, not create new ones. For example, it does not provide a way to create new characters in a font. (you can add characters to a font using Fontconvert, though; see section 8.1.2 Character selection options). In terms of its interaction with the other font utilities, it is most useful for making character shapes more amenable to Limn's outline fitting (see section 10. Limn).
13.1 XBfe usage How to edit fonts. 13.2 Invoking XBfe Command-line options.