Preferences Dialog

AutoWidthSync
Whether you want the widths of accented characters to track the width of the base character (so if you modify the width of A then the width of À will automagically change, if À is built as a reference to A and a reference to grave)
AutoLBearingSync
Whether you want left side bearings of accented characters to track the left side bearing of base characters (so if you shift A left, then the accent in À will also be shifted left)
AutoHint
Whether characters should be automagically hinted before a bitmap character is generated (improves the quality of the bitmap)
LocalEncoding
The default encoding used by the operating system (ie. text that is pasted into pfaedit will be assumed to be in this encoding). If you select "Default" here, pfaedit will attempt to guess the correct encoding by looking at: LC_MESSAGES, LC_ALL, LANG environment variables.
NewCharset
The default encoding used to create new fonts. Normally this is ISO 8859-1.
ItalicConstrained
Whether constrained motion in the character view should allow motion parallel to the italic angle as well as horizontal and vertical.
AccentOffsetPercent
The amount of space (as a percentage of the em-square) that should be placed between an accent and the character below it by the Build Accented Character command.
AccentCenterBottom
Whether accents should be positioned over letters based on the center of the accent, or on the center of the bottom of the accent.
GreekFixup
Whether to accept Adobe's naming conventions for greek letters, or to make them a bit more expected.
ArrowMoveSize
The number of em-units an arrow key will move a selected point in the character view.
SnapDistance
The maximum distance at which pointer motion in the character view will be snapped to an interesting object (ie. a point, baseline, width line, etc.)

Foundry Name
Used in generating bdf files (part of the X Windows font naming convention).
TTFFoundry
Similar to the above except that it is used inside ttf files (the achVendID field of the OS/2 table) and is limitted to 4 characters.
XUID-Base
The base "XUID". Should uniquely identify the user's organization. If present then every new font will be given an XUID generated by appending a random number to the end of this string (which should consist of a set of numbers separated by spaces). Whenever a postscript font is generated then this last number will be incremented by 1.
AskBDFResolution
Normally PfaEdit will guess at what screen resolution you intend based on the pixel size of the font (ie. 17 pixel fonts are usually 100dpi (12pt) and 12 pixel fonts are usually 75dpi), but sometimes you will have more esoteric desires. Setting this will give you more control, but you have to click through another dlg.
DumpGlyphMap
Sometimes it is useful to have a mapping from ttf (or otf) glyph ID to character name. If you turn this on, then each time you generate a ttf/otf font you will also get a file with extension .g2n containing this mapping.
AutotraceArgs
This allows you to specify any arguments you want passed to the autotrace program. Don't try to pass something that will change the input or output format or set input or output files.
AutotraceAsk
If this is set then each time autotrace is invoked it will ask you for arguments.
MfArgs
This is the command passed to the mf (MetaFont) program which controls conversion of .mf files into bitmaps.
MfClearBg
Loading a .mf font is a multi step process, first a bitmap font is generated, it is loaded into the background, then autotrace is invoked to trace around the backgrounds. These background bitmaps can take up a lot of space and you may not want them after they have been autotraced. Selecting this entry will remove those bitmaps from the font after they have been used.
MfShowErr
The mf program generates a fair amount of verbiage even when it is working correctly. And if it is working correctly you don't want to see those words. So normally PfaEdit suppresses messages from mf. But if something goes wrong you do want to see mf's output and setting this will allow you to do so.

This section of the dialog allows you to define built in scripts that will show up in the script menu. Each entry has two things associated with it, the menu name and a script file. The menu name will be the name of this entry inside the script menu, and the script file will be the filename of the file to be invoked. The "..." button allows you to browse for script files, which I think have extension .pe (but which can have whatever extension you prefer if you don't like my conventions).
A number of things that might be controlled from a preference window are controlled by X Resources.

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