Don't use symlink and update some files/projects

IB-7781, Fixes #480

Signed-off-by: Raul Metsma <[email protected]>

etc/Doxyfile.in

@@ -1,4 +1,4 @@
-# Doxyfile 1.9.5
+# Doxyfile 1.9.7
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -86,7 +86,7 @@ CREATE_SUBDIRS         = NO
 # level increment doubles the number of directories, resulting in 4096
 # directories at level 8 which is the default and also the maximum value. The
 # sub-directories are organized in 2 levels, the first level always has a fixed
-# numer of 16 directories.
+# number of 16 directories.
 # Minimum value: 0, maximum value: 8, default value: 8.
 # This tag requires that the tag CREATE_SUBDIRS is set to YES.
 
@@ -363,6 +363,17 @@ MARKDOWN_SUPPORT       = YES
 
 TOC_INCLUDE_HEADINGS   = 5
 
+# The MARKDOWN_ID_STYLE tag can be used to specify the algorithm used to
+# generate identifiers for the Markdown headings. Note: Every identifier is
+# unique.
+# Possible values are: DOXYGEN Use a fixed 'autotoc_md' string followed by a
+# sequence number starting at 0. and GITHUB Use the lower case version of title
+# with any whitespace replaced by '-' and punctations characters removed..
+# The default value is: DOXYGEN.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+MARKDOWN_ID_STYLE      = DOXYGEN
+
 # When enabled doxygen tries to link words that correspond to documented
 # classes, or namespaces to their corresponding documentation. Such a link can
 # be prevented in individual cases by putting a % sign in front of the word or
@@ -487,6 +498,14 @@ LOOKUP_CACHE_SIZE      = 0
 
 NUM_PROC_THREADS       = 1
 
+# If the TIMESTAMP tag is set different from NO then each generated page will
+# contain the date or date and time when the page was generated. Setting this to
+# NO can help when comparing the output of multiple runs.
+# Possible values are: YES, NO, DATETIME and DATE.
+# The default value is: NO.
+
+TIMESTAMP              = YES
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -568,7 +587,8 @@ HIDE_UNDOC_MEMBERS     = NO
 # If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
 # undocumented classes that are normally visible in the class hierarchy. If set
 # to NO, these classes will be included in the various overviews. This option
-# has no effect if EXTRACT_ALL is enabled.
+# will also hide undocumented C++ concepts if enabled. This option has no effect
+# if EXTRACT_ALL is enabled.
 # The default value is: NO.
 
 HIDE_UNDOC_CLASSES     = NO
@@ -859,11 +879,26 @@ WARN_IF_INCOMPLETE_DOC = YES
 
 WARN_NO_PARAMDOC       = NO
 
+# If WARN_IF_UNDOC_ENUM_VAL option is set to YES, doxygen will warn about
+# undocumented enumeration values. If set to NO, doxygen will accept
+# undocumented enumeration values. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: NO.
+
+WARN_IF_UNDOC_ENUM_VAL = NO
+
 # 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
 # then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
 # at the end of the doxygen process doxygen will return with a non-zero status.
-# Possible values are: NO, YES and FAIL_ON_WARNINGS.
+# If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS_PRINT then doxygen behaves
+# like FAIL_ON_WARNINGS but in case no WARN_LOGFILE is defined doxygen will not
+# write the warning messages in between other messages but write them at the end
+# of a run, in case a WARN_LOGFILE is defined the warning messages will be
+# besides being in the defined file also be shown at the end of a run, unless
+# the WARN_LOGFILE is defined as - i.e. standard output (stdout) in that case
+# the behavior will remain as with the setting FAIL_ON_WARNINGS.
+# Possible values are: NO, YES, FAIL_ON_WARNINGS and FAIL_ON_WARNINGS_PRINT.
 # The default value is: NO.
 
 WARN_AS_ERROR          = NO
@@ -1014,9 +1049,6 @@ EXCLUDE_PATTERNS       = */crypto/Connect.* \
 # output. The symbol name can be a fully qualified name, a word, or if the
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
 # ANamespace::AClass, ANamespace::*Test
-#
-# Note that the wildcards are matched against the file with absolute path, so to
-# exclude all test directories use the pattern */test/*
 
 EXCLUDE_SYMBOLS        = digidoc::*Private \
                          digidoc::asic \
@@ -1220,10 +1252,11 @@ VERBATIM_HEADERS       = NO
 
 ALPHABETICAL_INDEX     = YES
 
-# In case all classes in a project start with a common prefix, all classes will
-# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
-# can be used to specify a prefix (or a list of prefixes) that should be ignored
-# while generating the index headers.
+# The IGNORE_PREFIX tag can be used to specify a prefix (or a list of prefixes)
+# that should be ignored while generating the index headers. The IGNORE_PREFIX
+# tag works for classes, function and member names. The entity will be placed in
+# the alphabetical list under the first letter of the entity name that remains
+# after removing the prefix.
 # This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
 
 IGNORE_PREFIX          =
@@ -1302,7 +1335,12 @@ HTML_STYLESHEET        =
 # Doxygen will copy the style sheet files to the output directory.
 # Note: The order of the extra style sheet files is of importance (e.g. the last
 # style sheet in the list overrules the setting of the previous ones in the
-# list). For an example see the documentation.
+# list).
+# Note: Since the styling of scrollbars can currently not be overruled in
+# Webkit/Chromium, the styling will be left out of the default doxygen.css if
+# one or more extra stylesheets have been specified. So if scrollbar
+# customization is desired it has to be added explicitly. For an example see the
+# documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_EXTRA_STYLESHEET  = @CMAKE_SOURCE_DIR@/etc/Doxyfile.css
@@ -1318,17 +1356,13 @@ HTML_EXTRA_STYLESHEET  = @CMAKE_SOURCE_DIR@/etc/Doxyfile.css
 HTML_EXTRA_FILES       =
 
 # The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
-# should be rendered with a dark or light theme. Default setting AUTO_LIGHT
-# enables light output unless the user preference is dark output. Other options
-# are DARK to always use dark mode, LIGHT to always use light mode, AUTO_DARK to
-# default to dark mode unless the user prefers light mode, and TOGGLE to let the
-# user toggle between dark and light mode via a button.
-# Possible values are: LIGHT Always generate light output., DARK Always generate
-# dark output., AUTO_LIGHT Automatically set the mode according to the user
-# preference, use light mode if no preference is set (the default)., AUTO_DARK
-# Automatically set the mode according to the user preference, use dark mode if
-# no preference is set. and TOGGLE Allow to user to switch between light and
-# dark mode via a button..
+# should be rendered with a dark or light theme.
+# Possible values are: LIGHT always generate light mode output, DARK always
+# generate dark mode output, AUTO_LIGHT automatically set the mode according to
+# the user preference, use light mode if no preference is set (the default),
+# AUTO_DARK automatically set the mode according to the user preference, use
+# dark mode if no preference is set and TOGGLE allow to user to switch between
+# light and dark mode via a button.
 # The default value is: AUTO_LIGHT.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
@@ -1364,15 +1398,6 @@ HTML_COLORSTYLE_SAT    = 100
 
 HTML_COLORSTYLE_GAMMA  = 80
 
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting this
-# to YES can help to show when doxygen was last run and thus if the
-# documentation is up to date.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_TIMESTAMP         = YES
-
 # If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
 # documentation will contain a main index with vertical navigation menus that
 # are dynamically created via JavaScript. If disabled, the navigation index will
@@ -1522,6 +1547,16 @@ BINARY_TOC             = NO
 
 TOC_EXPAND             = NO
 
+# The SITEMAP_URL tag is used to specify the full URL of the place where the
+# generated documentation will be placed on the server by the user during the
+# deployment of the documentation. The generated sitemap is called sitemap.xml
+# and placed on the directory specified by HTML_OUTPUT. In case no SITEMAP_URL
+# is specified no sitemap is generated. For information about the sitemap
+# protocol see https://www.sitemaps.org
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SITEMAP_URL            =
+
 # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
 # QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
 # can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
@@ -2010,9 +2045,16 @@ PDF_HYPERLINKS         = YES
 
 USE_PDFLATEX           = YES
 
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
-# command to the generated LaTeX files. This will instruct LaTeX to keep running
-# if errors occur, instead of asking the user for help.
+# The LATEX_BATCHMODE tag ignals the behavior of LaTeX in case of an error.
+# Possible values are: NO same as ERROR_STOP, YES same as BATCH, BATCH In batch
+# mode nothing is printed on the terminal, errors are scrolled as if <return> is
+# hit at every error; missing files that TeX tries to input or request from
+# keyboard input (\read on a not open input stream) cause the job to abort,
+# NON_STOP In nonstop mode the diagnostic message will appear on the terminal,
+# but there is no possibility of user interaction just like in batch mode,
+# SCROLL In scroll mode, TeX will stop only for missing files to input or if
+# keyboard input is necessary and ERROR_STOP In errorstop mode, TeX will stop at
+# each error, asking for user intervention.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
@@ -2033,14 +2075,6 @@ LATEX_HIDE_INDICES     = NO
 
 LATEX_BIB_STYLE        = plain
 
-# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
-# page will contain the date and time when the page was generated. Setting this
-# to NO can help when comparing the output of multiple runs.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_TIMESTAMP        = NO
-
 # The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
 # path from which the emoji images will be read. If a relative path is entered,
 # it will be relative to the LATEX_OUTPUT directory. If left blank the
@@ -2206,7 +2240,7 @@ DOCBOOK_OUTPUT         = docbook
 #---------------------------------------------------------------------------
 
 # If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
-# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# AutoGen Definitions (see https://autogen.sourceforge.net/) file that captures
 # the structure of the code including all documentation. Note that this feature
 # is still experimental and incomplete at the moment.
 # The default value is: NO.
@@ -2377,16 +2411,9 @@ EXTERNAL_GROUPS        = YES
 EXTERNAL_PAGES         = YES
 
 #---------------------------------------------------------------------------
-# Configuration options related to the dot tool
+# Configuration options related to diagram generator tools
 #---------------------------------------------------------------------------
 
-# You can include diagrams made with dia in doxygen documentation. Doxygen will
-# then run dia to produce the diagram and insert it in the documentation. The
-# DIA_PATH tag allows you to specify the directory where the dia binary resides.
-# If left empty dia is assumed to be found in the default search path.
-
-DIA_PATH               =
-
 # If set to YES the inheritance and collaboration graphs will hide inheritance
 # and usage relations if the target is undocumented or is not a class.
 # The default value is: YES.
@@ -2395,7 +2422,7 @@ HIDE_UNDOC_RELATIONS   = YES
 
 # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
 # available from the path. This tool is part of Graphviz (see:
-# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# https://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
 # Bell Labs. The other options in this section have no effect if this option is
 # set to NO
 # The default value is: NO.
@@ -2448,13 +2475,15 @@ DOT_NODE_ATTR          = "shape=box,height=0.2,width=0.4"
 
 DOT_FONTPATH           =
 
-# If the CLASS_GRAPH tag is set to YES (or GRAPH) then doxygen will generate a
-# graph for each documented class showing the direct and indirect inheritance
-# relations. In case HAVE_DOT is set as well dot will be used to draw the graph,
-# otherwise the built-in generator will be used. If the CLASS_GRAPH tag is set
-# to TEXT the direct and indirect inheritance relations will be shown as texts /
-# links.
-# Possible values are: NO, YES, TEXT and GRAPH.
+# If the CLASS_GRAPH tag is set to YES or GRAPH or BUILTIN then doxygen will
+# generate a graph for each documented class showing the direct and indirect
+# inheritance relations. In case the CLASS_GRAPH tag is set to YES or GRAPH and
+# HAVE_DOT is enabled as well, then dot will be used to draw the graph. In case
+# the CLASS_GRAPH tag is set to YES and HAVE_DOT is disabled or if the
+# CLASS_GRAPH tag is set to BUILTIN, then the built-in generator will be used.
+# If the CLASS_GRAPH tag is set to TEXT the direct and indirect inheritance
+# relations will be shown as texts / links.
+# Possible values are: NO, YES, TEXT, GRAPH and BUILTIN.
 # The default value is: YES.
 
 CLASS_GRAPH            = TEXT
@@ -2595,7 +2624,7 @@ DIR_GRAPH_MAX_DEPTH    = 1
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
 # generated by dot. For an explanation of the image formats see the section
 # output formats in the documentation of the dot tool (Graphviz (see:
-# http://www.graphviz.org/)).
+# https://www.graphviz.org/)).
 # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
 # to make the SVG files visible in IE 9+ (other browsers do not have this
 # requirement).
@@ -2632,11 +2661,12 @@ DOT_PATH               =
 
 DOTFILE_DIRS           =
 
-# The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the \mscfile
-# command).
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
 
-MSCFILE_DIRS           =
+DIA_PATH               =
 
 # The DIAFILE_DIRS tag can be used to specify one or more directories that
 # contain dia files that are included in the documentation (see the \diafile
@@ -2713,3 +2743,19 @@ GENERATE_LEGEND        = YES
 # The default value is: YES.
 
 DOT_CLEANUP            = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. If the MSCGEN_TOOL tag is left empty (the default), then doxygen will
+# use a built-in version of mscgen tool to produce the charts. Alternatively,
+# the MSCGEN_TOOL tag can also specify the name an external tool. For instance,
+# specifying prog as the value, doxygen will call the tool as prog -T
+# <outfile_format> -o <outputfile> <inputfile>. The external tool should support
+# output file formats "png", "eps", "svg", and "ismap".
+
+MSCGEN_TOOL            =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the \mscfile
+# command).
+
+MSCFILE_DIRS           =

examples/android/app/src/main/AndroidManifest.xml

@@ -2,8 +2,6 @@
 <manifest xmlns:android="http://schemas.android.com/apk/res/android">
 
     <uses-permission android:name="android.permission.INTERNET" />
-    <uses-permission android:name="android.permission.READ_EXTERNAL_STORAGE" />
-    <uses-permission android:name="android.permission.WRITE_EXTERNAL_STORAGE" />
 
     <application
         android:allowBackup="true"

examples/android/app/src/main/java/ee/ria/libdigidocpp/MainActivity.java

@@ -26,6 +26,8 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.security.cert.X509Certificate;
 import java.sql.Timestamp;
 import java.util.Objects;
@@ -45,16 +47,6 @@ public class MainActivity extends Activity {
 		System.loadLibrary("digidoc_java");
 	}
 
-	static private void saveToFile(InputStream in, String path) throws IOException {
-		try (FileOutputStream out = new FileOutputStream(path)) {
-			byte[] buffer = new byte[10240];
-			int count;
-			while ((count = in.read(buffer)) != -1) {
-				out.write(buffer, 0, count);
-			}
-		}
-	}
-
 	@Override
 	protected void onCreate(Bundle savedInstanceState) {
 		super.onCreate(savedInstanceState);
@@ -67,14 +59,14 @@ protected void onCreate(Bundle savedInstanceState) {
 			try (ZipInputStream zis = new ZipInputStream(getResources().openRawResource(R.raw.schema))) {
 				ZipEntry ze;
 				while ((ze = zis.getNextEntry()) != null) {
-					saveToFile(zis, cache + "/" + ze.getName());
+					Files.copy(zis, Paths.get(cache, ze.getName()));
 				}
 			}
 			try (InputStream in = getResources().openRawResource(R.raw.test)) {
-				saveToFile(in, cache + "/test.bdoc");
+				Files.copy(in, Paths.get(cache, "test.bdoc"));
 			}
 			try (ByteArrayInputStream bin = new ByteArrayInputStream(new byte[] {})) {
-				saveToFile(bin, cache + "/EE_T.xml");
+				Files.copy(bin, Paths.get(cache, "EE_T.xml"));
 			}
 		} catch (IOException e) {
 			e.printStackTrace();
@@ -224,7 +216,7 @@ private void runTest(File path) {
 			}
 
 			try (FileInputStream in = new FileInputStream(cache + "/digidocpp.log")) {
-				saveToFile(in, Environment.getExternalStorageDirectory().getAbsolutePath() + "/digidocpp.log");
+				Files.copy(in, Paths.get(Environment.getExternalStorageDirectory().getAbsolutePath(), "digidocpp.log"));
 			}
 			try (FileOutputStream out = new FileOutputStream(Environment.getExternalStorageDirectory().getAbsolutePath() + "/result.json")) {
 				out.write(r.toString().getBytes(StandardCharsets.UTF_8));
@@ -285,7 +277,7 @@ protected Exception doInBackground(Void... tmp) {
 					ZipEntry ze;
 					while ((ze = zis.getNextEntry()) != null) {
 						try {
-							saveToFile(zis, path + "/" + ze.getName());
+							Files.copy(zis, Paths.get(path.getPath(), ze.getName()));
 						} catch (Exception e) {
 							e.printStackTrace();
 						}