Index: /branches/elixir/Ohana/src/shell/Makefile
===================================================================
--- /branches/elixir/Ohana/src/shell/Makefile	(revision 2476)
+++ /branches/elixir/Ohana/src/shell/Makefile	(revision 2476)
@@ -0,0 +1,43 @@
+include ../../Configure
+HOME 	=	$(ROOT)/src/shell
+
+DESTBIN	=	$(LBIN)
+
+shell:
+
+default: install
+
+DADS = \
+dads.cleanup
+
+GENERAL = \
+block checkdisks dumptape \
+fits2jpeg gopsfphot gosexphot \
+setpath scattercorrection \
+vncstart vnccheck
+
+IMSTATS = \
+irsex sexstats
+
+MKDETREND = \
+detstats rm.elixir
+
+REALTIME = \
+el_plots elixir.fork elixir.launch \
+getfocus getseeing gettemps mkjpeg
+
+SKYPROBE = \
+sp_command sp_phot \
+sp_plots sp_sexphot
+
+CODE = $(DADS) $(GENERAL) $(IMSTATS) $(MKDETREND) $(POSTRUN) $(PTOLEMY) $(REALTIME) $(SKYPROBE)
+
+install:
+	for file in $(CODE); do \
+	(chmod +x src/$$file && cd $(DESTBIN) && rm -f $$file && ln -s $(HOME)/src/$$file .); \
+	done
+
+# utilities #################################################
+clean:	
+	rm -f `find . -name "*~"`
+	rm -f `find . -name "#*"`
Index: /branches/elixir/Ohana/src/shell/doc/flips.notes
===================================================================
--- /branches/elixir/Ohana/src/shell/doc/flips.notes	(revision 2476)
+++ /branches/elixir/Ohana/src/shell/doc/flips.notes	(revision 2476)
@@ -0,0 +1,51 @@
+
+Some of the Elixir scripts call Flips programs.  Here is a list of the
+programs in Flips being used by Elixir:
+
+fr.defringe   : flipsrun (imcombred)
+fr.gtfringe   : flipsrun (imstat)
+defringe      : flipsrun (imcombred)
+doflips       : flatccd
+doflips       : darkccd
+flatten.flips : redccd 
+fr.mkrough    : flipsrun (imcombred)
+fr.smooth     : flipsrun (imfilter)
+gtfringe      : flipsrun (imstat)
+
+noni: file *
+RCS:            directory
+block:          C shell script text
+checkdisks:     C shell script text
+dads.cleanup:   C shell script text
+dads.remef:     C shell script text  - to be deprecated?
+dads.split:     C shell script text  - to be deprecated
+defringe:       C shell script text  - perl
+detstats:       C shell script text  - (mkdetrend)
+doflips:        C shell script text  - perl/detflips
+dumptape:       C shell script text
+el_plots:       C shell script text
+elixir.fork:    C shell script text
+elixir.launch:  C shell script text
+fits2jpeg:      C shell script text
+flatten.flips:  C shell script text  - perl
+flatten.subaru: C shell script text  - old
+fr.defringe:    C shell script text  - perl
+fr.mkrough:     C shell script text  - perl/detflips
+fr.smooth:      C shell script text  - perl TBD
+getfocus:       C shell script text
+getfringe:      bash shell script    - perl
+getseeing:      C shell script text
+gettemps:       C shell script text
+gopsfphot:      C shell script text
+gosexphot:      C shell script text
+irsex:          C shell script text
+mk.ptlist:      C shell script text
+mkjpeg:         C shell script text
+pt.export:      C shell script text
+rm.elixir:      C shell script text
+setpath:        C shell script text
+sexstats:       C shell script text
+sp_command:     C shell script text
+sp_phot:        C shell script text
+sp_plots:       C shell script text
+sp_sexphot:     C shell script text
Index: /branches/elixir/Ohana/src/shell/doc/notes.txt
===================================================================
--- /branches/elixir/Ohana/src/shell/doc/notes.txt	(revision 2476)
+++ /branches/elixir/Ohana/src/shell/doc/notes.txt	(revision 2476)
@@ -0,0 +1,113 @@
+block			general
+checkdisks		CFHT specific
+dads.cleanup		
+dads.remef		
+dads.split		
+defringe		N CCDs, CFH12K Coord file
+detrend			Not Used?
+detstats		OK (check mana scripts)
+doflips			OK
+dumptape		
+elixir.fork		
+elixir.grab		
+elixir.report		
+fits2jpeg		
+fixdetrend		
+flatten.flips		OK
+flatten.mana		OK	
+focusstats		
+fr.ckfile		Not Used
+fr.defringe		N CCDs (check mana scripts)
+fr.mkimage		OK
+fr.mkrough		OK
+fr.mkstats		(check scripts)
+fr.smooth		Scale is CCD dependent
+fr.stats		OK
+getfocus		
+getseeing		
+gettemps		
+gopsfphot		
+gosexphot		
+gtfringe		(sh) OK
+imstats			CCD size specific -- should use DETSEC
+merge.lists		OK
+mk2d			Not Used
+mkjpeg			(realtime) N CCD specific
+normalize		OK
+normalize.invert	-
+phot.by.night		
+pt.export		(ptolemy export process)
+rm.elixir		(drop & convert to the exit status method)
+setpath			unused?
+sexstats		OK
+skyprobephot		
+split.mef		OK
+spphot			
+
+-
+
+cfht.names		a
+checkconfig		CFHT specific
+ckastrom		
+ckdetrend		
+ckphotom		
+ckrunid			
+ckvalid			
+clear.rawdir		
+create.imlists		nut used
+create.subset		OK
+dads.detrend		
+dads.jpeg		
+dads.keywords		
+darktime.cfht		CFH12K specific -- these curves must be measured for a new device!
+fixlists		
+fl.split2mef		not used?
+fr.detrend		Nccds from gt_names -- more general encapsulation
+fr.gtstats		Nccds
+fr.medbin		Nccds
+fr.medbin.spline	Nccds
+fr.mklists		OK
+fr.select		
+fr.subset		
+get.standards		
+grab.keywords		
+images.names		
+imclean.cfht		
+imselect		
+imstatqso		
+merge.lists		
+mkdetrend		
+mkfringe		
+mkptolemy.names		
+mktrans			
+mktreport		
+mosaic.merge		
+mosaic.stats		
+pt.run			
+seeingstats		
+validate		
+
+shell scripts that use awk -v (convert to perl):
+defringe
+fr.defringe
+fr.smooth
+gtfringe   (convert from sh anyway)
+
+shell scripts which use CFH12K dependent things:
+
+defringe		N CCDs, CFH12K Coord file
+detstats		(check mana scripts)
+fr.ckfile		Nccds
+fr.defringe		N CCDs (check mana scripts)
+fr.mkimage		(check scripts)
+fr.mkstats		(check scripts)
+fr.smooth		Scale is CCD dependent
+fr.stats		(check scripts)
+imstats			CCD size specific -- should use DETSEC
+normalize		OK
+split.mef		CCD size specific
+
+(watch out for header keywords -- make a complete dictionary)
+
+shell -> perl
+split.mef
Index: /branches/elixir/Ohana/src/shell/doc/programs.txt
===================================================================
--- /branches/elixir/Ohana/src/shell/doc/programs.txt	(revision 2476)
+++ /branches/elixir/Ohana/src/shell/doc/programs.txt	(revision 2476)
@@ -0,0 +1,61 @@
+block			: x
+checkdisks		: x
+ckastro			: x
+dads.cleanup		: x
+dads.remef		: x
+dads.split		: +
+doflips			: x
+dumptape		: x
+elixir.fork		: x
+fits2jpeg		: x
+flatten.flips		: +
+flatten.subaru		: x (fake)
+gettemps		: x
+gopsfphot		: x
+gosexphot		: +
+imstats			: +
+merge.lists		: x
+mk2d			: x
+normalize		: x
+normalize.invert	: x
+phot.by.night		: x
+pt.export		: x
+rm.elixir		: x
+setpath			: x
+sexstats		: x
+detstats		: x
+
+getfocus		: [which chips should be camera-dependent]
+getseeing		: [which chip should be camera-dependent]
+mkjpeg			: [scale and ccd list should be camera-dependend]
+
+mk.ptlist		: - [ccds in list need to be ID, not N - add option to imsearch?]
+el_plots		: - (in script mana/elixir)
+
+skyprobe should have its own minimal config file
+
+skyprobephot		: [cleanup up config reference]
+sp_expose		: x
+split.mef		: x
+spphot			: [abstract RAWDIR, etc?]
+sp_plots		: [abstract plot directory?]
+
+mkfringe stuff:
+
+fr.fitstats		: +
+fr.imstats		: +
+fr.mkimage		: 
+fr.mkrough		: 
+fr.mkstats		: 
+fr.smooth		: 
+fr.stats		: 
+getfringe		: 
+defringe		: - (not very clean; might work)
+fr.defringe		: - (some major issues..)
+
+
+already checked:
+
+mode.imstats
+mode.sextract
+mode.flips