docs: move Doxyfile into subdir, refine makefile, use bigger logo

docs/Makefile

@@ -11,23 +11,23 @@ TRM_DIR=technical_reference_manual/
 # trailing / is important below
 DOXYGEN_DIR=doxygen/
 
-DOXYFILE=Doxyfile
+DOXYFILE=doxygen/Doxyfile
 
 FIJI_BIN_DIR=../bin
 
 UG_MAIN=fiji_user_guide
 TRM_MAIN=fiji_trm
 
-VIEW := "gnome-open"
+VIEW := xdg-open
 CWD := $(shell pwd)
 #FIND := $(shell find)
 UG_OUT  := $(UG_DIR)$(UG_MAIN).pdf
 TRM_OUT := $(TRM_DIR)$(TRM_MAIN).pdf
 DOXYGEN_OUT := $(DOXYGEN_DIR)html/index.html
 
-DOXYGEN_PREREQS := $(shell find $(FIJI_BIN_DIR) '(' -iname '*.pm' -o -iname '*.pl' ')') ../media/fiji_logo_50x50.png
+DOXYGEN_PREREQS := $(shell find $(FIJI_BIN_DIR) '(' -iname '*.pm' -o -iname '*.pl' ')') ../media/fiji_logo_56x56.png $(DOXYFILE)
 
-all: view
+all: ug trm doxygen
 
 view: view-ug view-trm view-doxygen
 
@@ -51,17 +51,20 @@ clean-trm:
 clean-doxygen:
 	rm -rf $(DOXYGEN_DIR)html
 
+ug: $(UG_OUT)
 $(UG_OUT):
 	$(MAKE) -C $(UG_DIR) $(UG_MAIN).pdf
 
 $(UG_DIR)$(UG_MAIN).aux :
 	$(MAKE) -C $(UG_DIR) fast
 
+trm: $(TRM_OUT)
 $(TRM_OUT): $(UG_DIR)$(UG_MAIN).aux
 	$(MAKE) -C $(TRM_DIR) $(TRM_MAIN).pdf
 
+doxygen: $(DOXYGEN_OUT)
 $(DOXYGEN_OUT): $(DOXYGEN_PREREQS)
 	doxygen $(DOXYFILE)
 
 
-.PHONY = clean clean-ug clean-trm view view-ug view-trm all fast
+.PHONY = all view view-ug view-trm view-doxygen clean clean-ug clean-trm ug trm doxygen