The documentation source is not a part of the tgz distribution archive. You must create a local clone of the Source Forge git repository to access and produce both html and pdf user help document(s).
You will have to install the dependency applications: autotools, doxygen and TeX/LateX. On a Debian based system:
$ sudo aptitude install autotools-dev
$ sudo aptitude install doxygen
$ sudo aptitude install texlive-latex-recommended
$ sudo aptitude install texlive-fonts-recommended
$ sudo aptitude install texlive-formats-extra
Create a suitable local directory for the git clone (change the directory location/name as appropriate for your installation).
$ cd
$ mkdir src.git
$ cd src.git
Clone the repository and change to the newly created clone source tree
$ git clone git://git.code.sf.net/p/fldigi/fldigi fldigi.git
$ cd fldigi.git
Prepare the clone for building objects
$ ls
$ autoreconf
$ automake --add-missing
Create the documentation
$ cd fldigi_doxygen
$ ./make_docs.sh
Doxygen and Latex will produce a lot of terminal output. Assuming no errors, the resulting html and pdf documents are in the fldigi_doxygen sub-directories:
$ ls pdf
FLDigi_4.1.00_Users_Manual.pdf FLDigi_4.1.00_Users_Manual_pdf.tgz
$ ls user_docs/html/index*
user_docs/html/index.html
The ''user_docs/html'' sub-directory contains the complete user documentation html tree (top level is index.html).