docs: fix order of compilation and hard-link pdfs into docs/

Also, change cross-document reference to look for the "other" pdf
file in the current directory instead of ../dir-name/

docs/Makefile

@@ -20,9 +20,8 @@ TRM_MAIN=fiji_trm
 
 VIEW := xdg-open
 CWD := $(shell pwd)
-#FIND := $(shell find)
-UG_OUT  := $(UG_DIR)$(UG_MAIN).pdf
-TRM_OUT := $(TRM_DIR)$(TRM_MAIN).pdf
+UG_OUT  := $(UG_MAIN).pdf
+TRM_OUT := $(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_56x56.png $(DOXYFILE)
@@ -32,39 +31,43 @@ all: ug trm doxygen
 view: view-ug view-trm view-doxygen
 
 view-ug: $(UG_OUT)
-	"$(VIEW)" "$(CWD)/$(UG_OUT)"
+	@"$(VIEW)" "$(CWD)/$(UG_OUT)"
 
 view-trm: $(TRM_OUT)
-	"$(VIEW)" "$(CWD)/$(TRM_OUT)"
+	@"$(VIEW)" "$(CWD)/$(TRM_OUT)"
 
 view-doxygen: $(DOXYGEN_OUT)
-	"$(VIEW)" "$(CWD)/$(DOXYGEN_OUT)"
+	@"$(VIEW)" "$(CWD)/$(DOXYGEN_OUT)"
 
 clean: clean-trm clean-ug clean-doxygen
 
 clean-ug:
-	$(MAKE) -C $(UG_DIR) clean
+	@$(MAKE) -C $(UG_DIR) clean
+	@rm -f $(UG_MAIN).pdf
 
 clean-trm:
-	$(MAKE) -C $(TRM_DIR) clean
+	@$(MAKE) -C $(TRM_DIR) clean
+	@rm -f $(TRM_MAIN).pdf
 
 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 $(UG_DIR) fast
+$(UG_OUT): $(TRM_DIR)$(TRM_MAIN).aux
+	@$(MAKE) -C $(UG_DIR) $(UG_MAIN).pdf
+	@ln -f $(UG_DIR)/$(UG_MAIN).pdf $(UG_MAIN).pdf
 
 trm: $(TRM_OUT)
 $(TRM_OUT): $(UG_DIR)$(UG_MAIN).aux
-	$(MAKE) -C $(TRM_DIR) $(TRM_MAIN).pdf
+	@$(MAKE) -C $(TRM_DIR) $(TRM_MAIN).pdf
+	@ln -f $(TRM_DIR)/$(TRM_MAIN).pdf $(TRM_MAIN).pdf
+
+%.aux:
+	@$(MAKE) -C $(dir $*) $(notdir $@)
 
 doxygen: $(DOXYGEN_OUT)
 $(DOXYGEN_OUT): $(DOXYGEN_PREREQS)
-	doxygen $(DOXYFILE)
+	@doxygen $(DOXYFILE)
 
 
 .PHONY = all view view-ug view-trm view-doxygen clean clean-ug clean-trm ug trm doxygen

docs/technical_reference_manual/fiji_trm.tex

 \input{../tex_common/header.tex}
 
-\externaldocument[UG:]{../user_guide/fiji_user_guide}
+\externaldocument[UG:]{../user_guide/fiji_user_guide}[fiji_user_guide.pdf]
 
 \def\title{FIJI Technical Reference Manual}
 

docs/tex_common/makefile.mk

@@ -17,18 +17,21 @@ TEX_OUT := $(OUTDIR)$(JOB).pdf
 all: view
 
 fast:
-	$(TEX) $(TEX_MAIN).tex
-	"$(VIEW)" "$(CWD)/$(TEX_OUT)"
+	@$(TEX) $(TEX_MAIN).tex
+	@"$(VIEW)" "$(CWD)/$(TEX_OUT)"
+
+$(TEX_MAIN).aux:
+	@$(TEX) $(TEX_MAIN).tex
+	@rm -f "$(CWD)/$(TEX_OUT)"
 
 view: $(TEX_OUT)
-	"$(VIEW)" "$(CWD)/$(TEX_OUT)"
+	@"$(VIEW)" "$(CWD)/$(TEX_OUT)"
 	
 clean:
-	rm -f $(TEX_OUT) $(OUTDIR)*.aux $(OUTDIR)*.bcf $(OUTDIR)*.bbl $(OUTDIR)*-blx.bib $(OUTDIR)*.run.xml $(OUTDIR)*.idx $(OUTDIR)*.ilg $(OUTDIR)*.lot $(OUTDIR)*.lof $(OUTDIR)*.lol $(OUTDIR)*.blg $(OUTDIR)*.alg $(OUTDIR)*.ind $(OUTDIR)*.toc $(OUTDIR)*.acl $(OUTDIR)*.acn $(OUTDIR)*.acr $(OUTDIR)*.out $(OUTDIR)*.log $(OUTDIR)*.gls $(OUTDIR)*.glo $(OUTDIR)*.glg $(OUTDIR)*.ist $(OUTDIR)*.brf $(OUTDIR)*.ver $(OUTDIR)*.hst $(OUTDIR)*.glsdefs
+	@rm -f $(TEX_OUT) $(OUTDIR)*.aux $(OUTDIR)*.bcf $(OUTDIR)*.bbl $(OUTDIR)*-blx.bib $(OUTDIR)*.run.xml $(OUTDIR)*.idx $(OUTDIR)*.ilg $(OUTDIR)*.lot $(OUTDIR)*.lof $(OUTDIR)*.lol $(OUTDIR)*.blg $(OUTDIR)*.alg $(OUTDIR)*.ind $(OUTDIR)*.toc $(OUTDIR)*.acl $(OUTDIR)*.acn $(OUTDIR)*.acr $(OUTDIR)*.out $(OUTDIR)*.log $(OUTDIR)*.gls $(OUTDIR)*.glo $(OUTDIR)*.glg $(OUTDIR)*.ist $(OUTDIR)*.brf $(OUTDIR)*.ver $(OUTDIR)*.hst $(OUTDIR)*.glsdefs
 
 PREREQS := $(wildcard *.tex *.bib content/*.tex img/*.tex img/*.pdf img/*.png ../tex_common/*.tex ../tex_common/img/*.tex)
-$(JOB).pdf: $(PREREQS)
-	$(TEX) $(TEX_MAIN)
+$(JOB).pdf: $(TEX_MAIN).aux $(PREREQS)
 # only run bibtex if there exist bib files
 ifneq (,$(filter %.bib,$(PREREQS)))
 	$(BIB) $(OUTDIR)$(JOB)

docs/user_guide/fiji_user_guide.tex

 \input{../tex_common/header.tex}
 \def\title{FIJI User Guide}
 
-\externaldocument[TRM:]{../technical_reference_manual/fiji_trm}
+\externaldocument[TRM:]{../technical_reference_manual/fiji_trm}[fiji_trm.pdf]
 
 \begin{document}
 \label{first_page}