Description: Make build reproducible
Author: Sascha Steinbiss <satta@debian.org> 
--- a/Makefile
+++ b/Makefile
@@ -16,6 +16,7 @@
 # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 #
 
+CURDIR=.
 INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj
 
 ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0)
@@ -728,7 +729,7 @@
 	$(V_DO)(echo '#ifndef GT_CONFIG_H' ;\
 	echo '#define GT_CONFIG_H' ;\
 	echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
-	echo '#define GT_CFLAGS "$(EXP_CFLAGS) $(GT_CFLAGS)"' ;\
+	echo '#define GT_CFLAGS "$(subst $(shell pwd),.,$(EXP_CFLAGS)) $(subst $(shell pwd),.,$(GT_CFLAGS))"' ;\
 	echo '$(EXP_CPPFLAGS) $(GT_CPPFLAGS)' | \
 	sed -e 's/\([^\]\)"/\1\\"/g' -e 's/^"/\\"/g' -e 's/$$/"/' \
 	    -e 's/^/#define GT_CPPFLAGS "/'; \
@@ -927,7 +928,7 @@
         > www/genometools.org/htdocs/libgenometools.html
 	bin/gt gtscripts/gtdoc.lua -lua -html $(CURDIR) \
         > www/genometools.org/htdocs/docs.html
-ifdef SKETCH_EXTRA_BINARIES
+ifdef ___SKETCH_EXTRA_BINARIES
 	bin/examples/sketch_parsed gtdata/sketch/default.style \
           www/genometools.org/htdocs/images/parsed.png \
           testdata/eden.gff3
--- a/doc/manuals/annotationsketch.tex
+++ b/doc/manuals/annotationsketch.tex
@@ -51,6 +51,7 @@
 \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz}
 
 \date{11/07/2012}
+\pdftrailerid{}
 \begin{document}
 
 \maketitle
@@ -241,7 +242,7 @@
 We will call the second part (after the ``\texttt{|}'') of these track titles \emph{track identifier strings} in the rest of this document.
 
 \begin{figure}[ht]
-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect.png}}
+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect}}
 \caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.}
 \label{tsexample1}
 \end{figure}
@@ -271,7 +272,7 @@
 Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}).
 
 \begin{figure}[ht]
-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect.png}}
+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect}}
 \caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.}
 \label{tsexample2}
 \end{figure}
@@ -313,7 +314,7 @@
 This code results in the image shown in Fig.~\ref{tsexample3} :
 
 \begin{figure}[ht]
-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect.png}}
+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect}}
 \caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.}
 \label{tsexample3}
 \end{figure}
@@ -322,7 +323,7 @@
 There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ctexample1}.
 
 \begin{figure}[ht]
-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct.png}}
+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct}}
 \caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.}
 \label{ctexample1}
 \end{figure}
@@ -415,7 +416,7 @@
 Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2}
 
 \begin{figure}[ht]
-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2.png}}
+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2}}
 \caption{The example insertion site custom track (at the bottom), displaying three sample data points.}
 \label{ctexample2}
 \end{figure}
--- a/doc/manuals/genomediff.tex
+++ b/doc/manuals/genomediff.tex
@@ -60,6 +60,7 @@
 \end{tabular}}
 
 \date{02/10/2012}
+\pdftrailerid{}
 \begin{document}
 %\tsuhhfamily
 \maketitle
--- a/doc/manuals/hop.tex
+++ b/doc/manuals/hop.tex
@@ -33,6 +33,7 @@
         \end{tabular}}
 
 \date{15/05/2014}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/ltrdigest.tex
+++ b/doc/manuals/ltrdigest.tex
@@ -42,6 +42,7 @@
         \end{tabular}}
 
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/ltrharvest.tex
+++ b/doc/manuals/ltrharvest.tex
@@ -42,6 +42,7 @@
         \end{tabular}
         \end{tabular}}
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/mgth.tex
+++ b/doc/manuals/mgth.tex
@@ -38,6 +38,7 @@
          Germany\\[1cm]
         \end{tabular}}
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/packedindex.tex
+++ b/doc/manuals/packedindex.tex
@@ -39,6 +39,7 @@
         \end{tabular}
         \end{tabular}}
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/readjoiner.tex
+++ b/doc/manuals/readjoiner.tex
@@ -46,6 +46,7 @@
         \end{tabular}}
 
 \date{18/02/2014}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/repfind.tex
+++ b/doc/manuals/repfind.tex
@@ -29,6 +29,7 @@
         \end{tabular}}
 
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 This manual describes the options of the program \Repfind. It also gives
--- a/doc/manuals/tagerator.tex
+++ b/doc/manuals/tagerator.tex
@@ -23,6 +23,7 @@
         \end{tabular}}
 
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/manuals/tallymer.tex
+++ b/doc/manuals/tallymer.tex
@@ -96,6 +96,7 @@
         \end{tabular}}
 
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 This manual describes the \textit{Tallymer}-software, a collection of programs
--- a/doc/manuals/uniquesub.tex
+++ b/doc/manuals/uniquesub.tex
@@ -48,6 +48,7 @@
         \end{tabular}}
 
 \date{26/08/2013}
+\pdftrailerid{}
 \begin{document}
 \maketitle
 
--- a/doc/devguide/devguide.tex
+++ b/doc/devguide/devguide.tex
@@ -38,7 +38,7 @@
         \texttt{sascha@steinbiss.name}}}
 \date{18/02/2016}
 
-
+\pdftrailerid{}
 \begin{document}
 \maketitle
 \tableofcontents