Unbreak Doxygen configuration (#559)

* Unbreak Doxygen configuration

PROJECT_NAME goes into the title, don't scream with ALL CAPS here.
PROJECT_BRIEF also goes into the title. Trailing dots are not used
in English titles and do not look good.

JAVADOC_AUTOBRIEF set to YES because writing "@brief" is excessive
and some members do not use it (resulting in missing short docs).

OPTIMIZE_OUTPUT_FOR_C so that we don't have references to classes
and things like that. We use Doxygen for Themis Core.

TYPEDEF_HIDES_STRUCT set to YES because Themis code style uses
typedefs instead of C tags, so we prefer to not mention them.

INPUT should include the top-level README file and only Themis Core.
USE_MDFILE_AS_MAINPAGE makes sure that README is displayed.
FILE_PATTERNS have to be set explicitly, otherwise Doxygen does not
see our source code.

MACRO_EXPANSION, EXPAND_ONLY_PREDEF, and PREDEFINED are used to
hide pervasive API exporting macros from Doxygen output.

* Doxygen-friendly deprecations

Write these macros in a single line so that Doxygen preprocessor
strips them and does not break function definitions because of that.

Doxyfile

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "THEMIS"
+PROJECT_NAME           = Themis
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -44,7 +44,7 @@ PROJECT_NUMBER         =
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "Data security library for network communication and data storage."
+PROJECT_BRIEF          = "Data security library for network communication and data storage"
 
 # With the PROJECT_LOGO tag one can specify an logo or icon that is included in
 # the documentation. The maximum height of the logo should not exceed 55 pixels
@@ -177,7 +177,7 @@ SHORT_NAMES            = NO
 # description.)
 # The default value is: NO.
 
-JAVADOC_AUTOBRIEF      = NO
+JAVADOC_AUTOBRIEF      = YES
 
 # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
 # line (until the first dot) of a Qt-style comment as the brief description. If
@@ -242,7 +242,7 @@ TCL_SUBST              =
 # members will be omitted, etc.
 # The default value is: NO.
 
-OPTIMIZE_OUTPUT_FOR_C  = NO
+OPTIMIZE_OUTPUT_FOR_C  = YES
 
 # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
 # Python sources only. Doxygen will then generate output that is more tailored
@@ -382,7 +382,7 @@ INLINE_SIMPLE_STRUCTS  = NO
 # types are typedef'ed and only the typedef is referenced, never the tag name.
 # The default value is: NO.
 
-TYPEDEF_HIDES_STRUCT   = NO
+TYPEDEF_HIDES_STRUCT   = YES
 
 # The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
 # cache is used to resolve symbols given their name and scope. Since this can be
@@ -753,7 +753,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src
+INPUT                  = README.md src/soter src/themis
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -773,7 +773,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          =
+FILE_PATTERNS          = *.c *.h
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -889,7 +889,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1933,15 +1933,15 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
 # EXPAND_AS_DEFINED tags.
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES the includes files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -1973,7 +1973,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = THEMIS_API SOTER_API
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

src/themis/secure_message.h

@@ -154,8 +154,7 @@ themis_status_t themis_secure_message_verify(const uint8_t* public_key,
  * storage then THEMIS_BUFFER_TOO_SMALL will return and wrapped_message_length will store length of
  * buffer needed for wrapped message store
  */
-DEPRECATED("use 'themis_secure_message_encrypt' with private and public keys to encrypt message, "
-           "or 'themis_secure_message_sign' with private key to sign message")
+DEPRECATED("use 'themis_secure_message_encrypt' with private and public keys to encrypt message, or 'themis_secure_message_sign' with private key to sign message")
 THEMIS_API
 themis_status_t themis_secure_message_wrap(const uint8_t* private_key,
                                            size_t private_key_length,
@@ -182,8 +181,7 @@ themis_status_t themis_secure_message_wrap(const uint8_t* private_key,
  * THEMIS_BUFFER_TOO_SMALL will return and message_length will store length of buffer needed for
  * plain message store
  */
-DEPRECATED("use 'themis_secure_message_decrypt' with private and public key to decrypt message or "
-           "'themis_secure_message_verify' with public key to verify signed message")
+DEPRECATED("use 'themis_secure_message_decrypt' with private and public key to decrypt message or 'themis_secure_message_verify' with public key to verify signed message")
 THEMIS_API
 themis_status_t themis_secure_message_unwrap(const uint8_t* private_key,
                                              size_t private_key_length,