I have just finished an extensive overhaul of the HaloProfiler that includes a bunch of new features, as well as completely changes the running syntax.  Other than the addition of various new features, the main goals of this overhaul were:
1) to make the tool more general (mostly by removing hard-coded filtering by virial quantities), essentially allowing someone to profile a random list of points that may or may not be actual halos
Easy filtering of halos by virial quantities remains an option, but is now simply a specific instance of something more general and far more powerful: a halo filtering device that allow the user to create their own filter functions to comb through radial profile data and decide whether a halo meets certain criteria.

2) to remove the dependence on an additional parameter file for the various options.
The parameter file is now gone.  Most of the HaloProfiler parameters have been turned into instantiation keyword args.  The keyword list is now considerably longer, but the benefit is that the number of files needed to run this thing has been reduced from 2 (running script and par file) to just 1 (running script).  There are a large number of keywords options that are specific to either the profile or projection routines that are taken in at instantiation and stored as attributes.  This was done to keep those function calls simple.  I'm curious to know peoples' thoughts on whether these keyword args should stay put or move to the individual function calls.  Adding fields for profiling and projections have been moved to functions addProfile and addProjection.

Here is a brief list of the new features that I can remember:
 - the halo list read routine can be easily customized to read in columned ascii data of varying formats through the use of a dictionary (see attribute self.halo_list_format)
 - ability to change the function call, args, and kwargs for the halo finder
 - filter halo list with user-written filter functions (see new file for an example of a function to filter based on virial quantities)
 - extract and output scalar quantities from halos using the filter functions
 - pre-filter halos based on values in the initial halo list (skipping the profiling altogether and saving a load of time)
 - choose the axes to be projected (instead of hard-coded to all three)
 - easily select the list of halos to be projected (the total list, filtered list, a new file, or an actual list)

Before I commit all this, I'd like a little feedback, mostly on the migration of the par file parameters to keyword args.  I put three files in the pastebin for people to download.  I chose not to submit a diff since the changes were so sweeping.
The new (should go in yt/extensions with (an example script to run the new HaloProfiler)

I will try my best to write up full documentation for this as soon as possible, perhaps even today.

Please let me know what you think.