doxygen: update config and Makefile, use same config for html and man

Author: mgates3

DOCS/Doxyfile

@@ -784,7 +784,7 @@ CITE_BIB_FILES         =
 # messages are off.
 # The default value is: NO.
 
-QUIET                  = YES
+QUIET                  = NO
 
 # The WARNINGS tag can be used to turn on/off the warning messages that are
 # generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
@@ -817,7 +817,7 @@ WARN_IF_DOC_ERROR      = YES
 # EXTRACT_ALL is set to YES then this flag will automatically be disabled.
 # The default value is: NO.
 
-WARN_NO_PARAMDOC       = NO
+WARN_NO_PARAMDOC       = YES
 
 # If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
 # a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
@@ -854,7 +854,7 @@ WARN_LOGFILE           = output_err
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = . \
+INPUT                  = BLAS CBLAS SRC INSTALL TESTING \
                          DOCS/groups-usr.dox
 
 # This tag can be used to specify the character encoding of the source files
@@ -902,34 +902,14 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = CMAKE \
-                         DOCS \
-                         .svn \
-                         CBLAS/.svn \
-                         CBLAS/src/.svn \
-                         CBLAS/testing/.svn \
-                         CBLAS/example/.svn \
-                         CBLAS/include/.svn \
-                         BLAS/.svn \
-                         BLAS/SRC/.svn \
-                         BLAS/TESTING/.svn \
-                         SRC/.svn \
-                         SRC/VARIANTS/.svn \
-                         SRC/VARIANTS/LIB/.svn \
-                         SRC/VARIANTS/cholesky/.svn \
-                         SRC/VARIANTS/cholesky/RL/.svn \
-                         SRC/VARIANTS/cholesky/TOP/.svn \
-                         SRC/VARIANTS/lu/.svn \
-                         SRC/VARIANTS/lu/CR/.svn \
-                         SRC/VARIANTS/lu/LL/.svn \
-                         SRC/VARIANTS/lu/REC/.svn \
-                         SRC/VARIANTS/qr/.svn \
-                         SRC/VARIANTS/qr/LL/.svn \
-                         INSTALL/.svn \
-                         TESTING/.svn \
-                         TESTING/EIG/.svn \
-                         TESTING/MATGEN/.svn \
-                         TESTING/LIN/.svn
+# Exclude functions that are duplicated in BLAS and INSTALL, creating conflicts.
+EXCLUDE                = .git \
+                         .github \
+                         BLAS/SRC/lsame.f \
+                         BLAS/SRC/xerbla.f \
+                         BLAS/SRC/xerbla_array.f \
+                         INSTALL/slamchf77.f \
+                         INSTALL/dlamchf77.f \
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded