The free firstobject XML editor has some command line switches. Here is the summary; details are below.

Switch	Purpose
-new	open in a new instance of the editor (useful when single instance preference is selected)
-same	open in the existing instance of the editor
-watch "C:\event.log"	open file in read-only auto-reloading mode to view the tail of log files
-line 23	open file at a line
-offset 451	UTF-8 offset from beginning of document or from beginning of line if line is specified
-fromoffset 5	pre-select text from this offset to specified offset
-run script.foal:f arg1 arg2	execute the script without showing the editor

Examples:

foxe.exe "C:\XML examples\file.xml" -line 6

foxe.exe file.xml -line 6 -offset 5

foxe.exe -offset 240 -fromoffset 235 file.xml

foxe.exe -watch C:\event.log

foxe.exe -run C:\script.foal

foxe.exe -same file.xml

"C:\Program Files\firstobject\foxe.exe" -new file.xml

As of release 2.4.1 the free firstobject XML editor has a command line switch to run a script:

foxe -run "C:\foal scripts\script.foal"

It generates 2 files, foxe_err.txt and foxe_out.txt. The err file contains marked up information about the run and can help diagnose issues with running. The out file contains the output returned from the script in the return statement.

And with release 2.4.2 you can specify function and arguments, see below.

str NavigateIterativelyXYZ_Generated( CMarkup mDocToNavigate )
{
  mDocToNavigate.ResetPos();
  str sXML = mDocToNavigate.GetDocFormatted(0);
  return sXML;
}

foxe –run align0.foal input.xml output.xml

Update April 23, 2011: With release 2.4.2, it works the way it should (the way Garth described). The -run command line option passes any number of command line arguments into the parameters of the function in the foal script. For example (remember to use quotes if a path or argument contains spaces):

foxe -run "C:\foal scripts\script.foal" C:\in.xml C:\out.xml

Here is a script to format XML that works with the previous command line:

formatxml(str sInPath, str sOutPath)
{
  CMarkup m, r;
  r.AddElem( "load", sInPath );
  m.Load( sInPath );
  r.AddSubDoc( m.GetResult() );
  if ( ! m.SetDoc(m.GetDocFormatted()) )
    r.AddSubDoc( m.GetResult() );
  r.AddElem( "save", sOutPath );
  m.Save(sOutPath);
  r.AddSubDoc( m.GetResult() );
  return r;
}

Bascially this script just loads the input file, calls GetDocFormatted and saves to the output file (you could also add an argument to pass format flags). In addition it returns the results in case something goes awry you can see what happened in foxe_out.txt. If there is no problem, it might look like this:

<load>C:\in.xml</load>
<read encoding="UTF-8" length="31579"/>
<save>C:\out.xml</save>
<write encoding="UTF-8" length="29958"/>

If there are multiple functions in a script, you can name your entry function main to avoid confusion about which function is being called. You can also specify the entry function explicitly on the command line with :function at the end of the script filename. Specifying the function allows you to invoke multiple functions in one script from the command line. Here is an example of using the same script to perform different operations:

foxe -run C:\script.foal:extract London

foxe -run C:\script.foal:merge London "New York"

If you specify a function name that is not found in the script, there will be an indication at the bottom of foxe_err.txt that also indicates the entry point it would have used if you had not specified one:

<entry_point arg_count="2" not_found="gormatxml">formatxml</entry_point>

If you do not specify the function and there is no main function in the script, the last function with a matching number of arguments is called. It chooses the last matching function because functions earlier in the script tend to be subroutines since in FOAL you can only call functions below where they are defined. 

Thanks for the help on escaping the trailing backslash in the command line. I think you should be able to make the foxe.exe call wait using the START /WAIT command to launch it. By default batch files wait, but windowing programs do not so you have to use the START command in that case.