Docs: fix various links in documentation

 - links to footnotes were fixed by deferring the loading of hyperref until
   after footmisc.
 - some cross-document links were wrong

docs/technical_reference_manual/content/03-software.tex

@@ -2,7 +2,7 @@
 \label{sec:flow}
 
 This chapter sums up some concepts of the Perl classes used in the \ac{FIJI} framework.
-Their use in the complete tool flow and the respective interfaces to the vendor tools are described in detail in \Cref{UG:sec:flow} of the \ac{UG}.
+Their use in the complete tool flow and the respective interfaces to the vendor tools are described in detail in \hyperref[UG:sec:flow]{the \ac*{UG}}.
 You should consult the Doxygen documentation and source files for the details beyong the overview given below.
 
 \subsection{FIJI Settings}

docs/tex_common/header.tex

@@ -5,17 +5,6 @@
 
 \usepackage{xr-hyper} % cross-document references, cf. http://www.tex.ac.uk/FAQ-extref.html
 
-\usepackage[colorlinks=true,
-	        linkcolor=black,
-	        citecolor=black,
-	        filecolor=black,
-	        urlcolor=black,
-	        bookmarks=true,
-	        bookmarksopen=true,
-	        bookmarksopenlevel=3,
-	        plainpages=false,
-	        pdfpagelabels=true]{hyperref} 
-
 \usepackage[utf8]{inputenc}
 \usepackage[T1]{fontenc}
 \usepackage[ngerman,english]{babel}
@@ -90,6 +79,18 @@
 \definecolor{twgreen}{RGB}{0,146,110}
 \definecolor{twblue}{RGB}{10,143,217}
 
+% load hyperref relatively late to let it workaround numerous problems
+\usepackage[colorlinks=true,
+	        linkcolor=black,
+	        citecolor=black,
+	        filecolor=black,
+	        urlcolor=black,
+	        bookmarks=true,
+	        bookmarksopen=true,
+	        bookmarksopenlevel=3,
+	        plainpages=false,
+	        pdfpagelabels=true]{hyperref}
+
 % Caption package to define caption style of images, tables, etc. %
 \usepackage{caption}
 \captionsetup[table]{singlelinecheck=false}

docs/user_guide/content/07-runtime.tex

@@ -37,7 +37,7 @@ ID, or CRC mismatch) the \ac{FIC} nevertheless continues reading in the appropri
 amount of frames/bytes for a configuration. Only after the complete reception 
 of the expected number of bytes the \ac{FIC} reports the result back to the host. To 
 that end a \textit{CONF\_DONE} message is sent, possibly with some set error bits (see 
-\Cref{sec:f2h}).
+\hyperref[TRM:sec:f2h]{the \ac*{TRM}}).
 
 Upon the successful reception of a configuration, the DUT is reset by the \ac{FIC} 
 if requested. The \ac{FIC} then optionally waits for a trigger signal (again