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  set X11 resources for a wish application in an app-defaults file?
 Read the documentation for the option command.
Then you should consider something like the following - assume the program
name is xwf.

The following are two general purpose functions to put into a library:

# envVal envValName
#   Looks up the envValName environment variable and returns its
#   value, or {} if it does not exists
proc envVal {envValName} {
  global env
  if [info exists env($envValName)] {return $env($envValName)} {return {}}

# loadAppDefaults classNameList ?priority?
#   Searches for the app-default files corresponding to classNames in
#   the order specified by X Toolkit Intrinsics, and loads them with
#   the priority specified (default: startupFile).
proc loadAppDefaults {classNameList {priority startupFile}} {
  set filepath "[split [envVal XUSERFILESEARCHPATH] :] 
		[split [envVal XFILESEARCHPATH] :] 
  foreach i $classNameList {
    foreach j $filepath {
      if {[file exists $j/$i]} {
	option readfile $j/$i $priority; break

# Now, here is what you would put into xwf:

option add Tk.BoldFont "*-lucida sans-Bold-R-Normal-*-100-*" widgetDefault
loadAppDefaults {xwf XWF} userDefault

This sets a program default, then load any defaults specified in the user`s
default resources and finally any site or general app-defaults resource.  
Of course, you would want to add some xwf command line handling to allow 
the user to override things at execution time.