docs: reorganize documentation into modular structure

Split monolithic index.org into separate pages for CLI and Java API
usage with proper subdirectory organization. Convert org-mode links
from ID-based to CUSTOM_ID and file references for reliable HTML
export. Simplify build script output and fix language clarity issues
throughout. Update Maven dependency version to 1.8.

diff --git a/Tools/Update web site b/Tools/Update web site
index 86d62a0..a58ff9c 100755 (executable)
--- a/Tools/Update web site
+++ b/Tools/Update web site
@@ -1,5 +1,5 @@
 #!/bin/bash
 #!/bin/bash

-cd "${0%/*}"; if [ "$1" != "T" ]; then gnome-terminal -- "$0" T; exit; fi;
+cd "${0%/*}"; if [ "$1" != "T" ]; then gnome-terminal -e "'$0' T"; exit; fi;

 
 cd ..
 
 
 cd ..
 


@@ -61,58 +61,31 @@ export_org_files_to_html() {
 }
 
 build_visualization_graphs() {
 }
 
 build_visualization_graphs() {

-    echo "🎨 Generating class visualization graphs..."
-    echo "======================================="
-

     rm -rf doc/graphs/
     mkdir -p doc/graphs/
 
     rm -rf doc/graphs/
     mkdir -p doc/graphs/
 

-    # JavaInspect analyzing itself - meta visualization!
-    javainspect -j target/javainspect.jar -d doc/graphs/ -n "All classes" -t png
-    javainspect -j target/javainspect.jar -d doc/graphs/ -n "Inspector" -t png -w "eu.svjatoslav.inspector.*"
-    javainspect -j target/javainspect.jar -d doc/graphs/ -n "Java parser" -t png -w "eu.svjatoslav.inspector.java.*"
+    # Generate self-visualization of JavaInspect
+    javainspect -j target/javainspect.jar -d doc/graphs/ -n "All classes" -t png -w "eu.svjatoslav.inspector.java.*" -ho

 
 

-    # Generate index page for graphs

     meviz index -w doc/graphs/ -t "JavaInspect classes"
     meviz index -w doc/graphs/ -t "JavaInspect classes"

-
-    echo "✓ Visualization graphs generated"
-    echo ""

 }
 
 # Build project jar file and JavaDocs
 }
 
 # Build project jar file and JavaDocs

-echo "🔨 Building project..."
-echo "======================================="

 mvn clean package
 
 mvn clean package
 

-if [ $? -ne 0 ]; then
-    echo "✗ Maven build failed!"
-    echo ""
-    echo "Press ENTER to close this window."
-    read
-    exit 1
-fi
-
-echo "✓ Maven build completed"
-echo ""
-

 # Put generated JavaDoc HTML files to documentation directory
 # Put generated JavaDoc HTML files to documentation directory

-echo "📚 Copying JavaDocs..."
-echo "======================================="

 rm -rf doc/apidocs/
 cp -r target/apidocs/ doc/
 
 rm -rf doc/apidocs/
 cp -r target/apidocs/ doc/
 

-echo "✓ JavaDocs copied to doc/apidocs/"
-echo ""
-

 # Publish Emacs org-mode files into HTML format
 export_org_files_to_html
 
 # Generate nice looking code visualization diagrams
 build_visualization_graphs
 
 # Publish Emacs org-mode files into HTML format
 export_org_files_to_html
 
 # Generate nice looking code visualization diagrams
 build_visualization_graphs
 

+

 ## Upload assembled documentation to server
 echo "📤 Uploading to server..."
 ## Upload assembled documentation to server
 echo "📤 Uploading to server..."

-echo "======================================="

 rsync -avz --delete -e 'ssh -p 10006' doc/ \
       n0@www3.svjatoslav.eu:/mnt/big/projects/javainspect/
 
 rsync -avz --delete -e 'ssh -p 10006' doc/ \
       n0@www3.svjatoslav.eu:/mnt/big/projects/javainspect/
 


@@ -124,4 +97,4 @@ fi
 
 echo ""
 echo "Press ENTER to close this window."
 
 echo ""
 echo "Press ENTER to close this window."

-read
\ No newline at end of file
+read

diff --git a/doc/Usage from CLI/index.org b/doc/Usage from CLI/index.org
new file mode 100644 (file)
index 0000000..7311d6a
--- /dev/null
+++ b/doc/Usage from CLI/index.org
@@ -0,0 +1,105 @@
+:PROPERTIES:
+:CUSTOM_ID: usage-from-cli
+:END:
+#+SETUPFILE: ~/.emacs.d/org-styles/html/darksun.theme
+#+TITLE: JavaInspect - usage from commandline
+#+LANGUAGE: en
+#+LATEX_HEADER: \usepackage[margin=1.0in]{geometry}
+#+LATEX_HEADER: \usepackage{parskip}
+#+LATEX_HEADER: \usepackage[none]{hyphenat}
+
+#+OPTIONS: H:20 num:20
+#+OPTIONS: author:nil
+
+[[file:../index.org][Back to main documentation]]
+
+* Commandline arguments
+:PROPERTIES:
+:CUSTOM_ID: available-commandline-arguments
+:END:
+
+
+- -j (existing files)... :: JAR file(s) to render.
+
+- -c (existing directories)... :: Classpath directories
+
+- -n (string) :: Graph name. (default: "graph")
+
+- --debug :: Show debug info.
+
+- -h, --help :: Show commandline usage help.
+
+- -k :: Keep dot file.
+
+- -ho ::
+    Hide orphaned classes.
+
+- -w (one to many strings)... :: Whitelist glob(s).
+
+- -b (one to many strings)... :: Blacklist glob(s).
+
+- -r (one to many strings)... :: root class(es).
+
+- -d (existing directory) :: Target directory. Default is current directory.
+
+- -t (options: png, svg) :: Target image type. Default is: svg.
+
+* Specifying classes to render
+:PROPERTIES:
+:CUSTOM_ID: specifying-classes-to-render
+:END:
+
+A typical Java application has immense complexity. Beyond code written
+by the project's developers, there are typically many frameworks,
+libraries, and the Java standard library.
+
+Since JavaInspect uses reflection, it cannot easily distinguish between
+these sources. Usually you want to visualize only the code developed
+for your project, excluding frameworks like Spring. If you visualize
+all classes reachable from your project, the graph becomes huge and
+incomprehensible.
+
+JavaInspect can analyze compiled Java classes in two modes:
+1. Provide JAR files using the *-j* option.
+2. Provide filesystem directories as classpath roots using the *-c* option.
+
+JavaInspect uses the following algorithm to add classes to the graph:
+
+- All classes found in JAR files are added to the graph by default.
+- Classes found in filesystem directories are not added by default
+  unless explicitly referenced. (TODO: for consistency, these should
+  also be added by default)
+- If a whitelist is specified (*-w* option), classes not matching the
+  whitelist patterns are removed from the graph.
+- If a blacklist is specified (*-b* option), classes matching the
+  blacklist patterns are removed from the graph.
+- Root classes can be specified using the *-r* option. JavaInspect
+  recursively discovers all classes referenced by root classes and
+  adds them to the graph.
+
+* Examples
+:PROPERTIES:
+:CUSTOM_ID: examples
+:END:
+
+Visualize a Java JAR file with all classes, hiding orphaned classes:
+
+#+begin_src sh
+  javainspect \
+      -j target/sixth-3d-*-SNAPSHOT.jar \
+      -d doc/graphs/ \
+      -n "All classes" \
+      -t png -ho
+#+end_src
+
+Visualize a Java JAR file with a whitelist filter, hiding orphaned classes:
+
+#+begin_src sh
+  javainspect \
+      -j target/sixth-3d-*-SNAPSHOT.jar \
+      -d doc/graphs/ \
+      -n "GUI" \
+      -t png \
+      -w "eu.svjatoslav.sixth.e3d.gui.*" \
+      -ho
+#+end_src

diff --git a/doc/Usage via Java API/index.org b/doc/Usage via Java API/index.org
new file mode 100644 (file)
index 0000000..a44747b
--- /dev/null
+++ b/doc/Usage via Java API/index.org
@@ -0,0 +1,126 @@
+:PROPERTIES:
+:CUSTOM_ID: usage-via-java-api
+:END:
+#+SETUPFILE: ~/.emacs.d/org-styles/html/darksun.theme
+#+TITLE: JavaInspect - Usage via Java API
+#+LANGUAGE: en
+#+LATEX_HEADER: \usepackage[margin=1.0in]{geometry}
+#+LATEX_HEADER: \usepackage{parskip}
+#+LATEX_HEADER: \usepackage[none]{hyphenat}
+
+#+OPTIONS: H:20 num:20
+#+OPTIONS: author:nil
+
+[[file:../index.org][Back to main documentation]]
+
+* Overview
+:PROPERTIES:
+:CUSTOM_ID: overview
+:END:
+Classes to be visualized must be available in the classpath.
+
+To include JavaInspect in the same classpath as your projects, there are
+two approaches:
+
+1. Add JavaInspect as a dependency in your project.
+
+2. Create a new Java project specifically for visualizing other
+   projects, and include both JavaInspect and your project's binary
+   artifacts (JARs) in the classpath. Binary JARs (without source code)
+   are sufficient since JavaInspect operates via reflection.
+
+Write simple control/configuration code for each project. I typically
+place this code in JUnit test directories since it doesn't need to be
+compiled into the final product or artifact.
+
+The control code generally does the following:
+1. Create a graph object.
+2. Java reflection/classloaders do not provide a mechanism to discover
+   all classes under a package. Therefore, manually add at least some
+   classes to the graph. For each class added, JavaInspect recursively
+   inspects it and adds all referenced classes.
+3. Graphs can easily become very large and complex, so optionally filter
+   important code using classname [[https://en.wikipedia.org/wiki/Glob_(programming)][glob]] pattern blacklists and/or
+   whitelists.
+4. Optionally tune rendering parameters:
+   + Remove orphaned classes (classes with no references) from the graph.
+   + Specify target directory for generated files (default: current directory).
+   + Keep intermediate GraphViz DOT file for later inspection.
+5. Render the graph.
+
+* Examples
+** Example 1: Hand-picked objects
+:PROPERTIES:
+:CUSTOM_ID: example-1-individually-picked-objects
+:END:
+This example generates a class graph from hand-picked classes, visualizing
+JavaInspect itself.
+
+#+BEGIN_SRC java
+
+// Create graph
+final ClassGraph graph = new ClassGraph();
+
+// Add an object to the graph. JavaInspect detects the class from the object.
+graph.add(graph);
+
+// Also add a class directly.
+graph.add(Utils.class);
+
+// Keep the intermediate GraphViz DOT file for reference.
+graph.setKeepDotFile(true);
+
+// Generate an image named "JavaInspect.png" in the current directory
+graph.generateGraph("JavaInspect");
+
+#+END_SRC
+
+Compact version:
+#+BEGIN_SRC java
+new ClassGraph().add(randomObject, RandomClass.class)
+                .setKeepDotFile(true).generateGraph("JavaInspect");
+#+END_SRC
+
+Result:
+- Generated DOT file: [[file:../JavaInspect.dot][JavaInspect.dot]]
+- Generated PNG image: [[file:../JavaInspect.png][JavaInspect.png]]
+
+** Example 2: Embedded in another project
+:PROPERTIES:
+:CUSTOM_ID: example-2-graphviz-embedded-in-another-project
+:END:
+
+1. Download a [[https://www2.svjatoslav.eu/gitweb/?p=sixth.git;a=snapshot;h=HEAD;sf=tgz][Sixth project snapshot]].
+2. Inspect and run *DataGraph.java*.
+
+* Embedding JavaInspect in your Maven project
+:PROPERTIES:
+:CUSTOM_ID: embedding-javainspect-in-your-maven-project
+:END:
+
+Declare JavaInspect as dependency:
+#+BEGIN_SRC xml
+<dependencies>
+    ...
+    <dependency>
+        <groupId>eu.svjatoslav</groupId>
+        <artifactId>javainspect</artifactId>
+        <version>1.8</version>
+    </dependency>
+    ...
+</dependencies>
+#+END_SRC
+
+
+Add Maven repository to retrieve artifact from:
+#+BEGIN_SRC xml
+<repositories>
+    ...
+    <repository>
+        <id>svjatoslav.eu</id>
+        <name>Svjatoslav repository</name>
+        <url>https://www3.svjatoslav.eu/maven/</url>
+    </repository>
+    ...
+</repositories>
+#+END_SRC

diff --git a/doc/index.org b/doc/index.org
index 145282f..020b2b9 100644 (file)
--- a/doc/index.org
+++ b/doc/index.org
@@ -13,37 +13,28 @@
 :CUSTOM_ID: overview
 :END:
 
 :CUSTOM_ID: overview
 :END:
 

-*JavaInspect* utility simplifies understanding the computer program
-code by automatically visualizing its structure.
-
-[[https://www3.svjatoslav.eu/projects/sixth-3d/graphs/][See example produced graphs]] for [[https://www3.svjatoslav.eu/projects/sixth-3d/][Sixth 3D - 3D engine project]].
-
-JavaInspect can be used as a [[id:acf1896a-74b4-4914-acf6-a77075e07f25][standalone commandline utility]] as well as
-[[id:bbeeffc8-3767-440d-8d93-ec9124dd60ee][java library]]. JavaInspect uses primarily Java built-in reflection to
-discover and visualize any part of Java program.
-
-JavaInspect currently has no graphical user interface, configuration
-files, embedded scripting support, direct Maven, Gradle or Ant
-integration. See [[id:2ad2889e-6c95-4662-b3f4-2c341fc74522][usage]] to learn how to instuct Javainspect what to do.
-
-After discovering application structure and optionally filtering out
-unimportant parts, JavaInspect produces GraphViz dot file that
-describes data to be visualized. Then launches [[https://graphviz.org/][GraphViz]] to generate
-bitmap graph in PNG or SVG format.
-
-Notes:
-+ JavaInspect is developed and tested so far only on GNU/Linux.
+*JavaInspect* simplifies understanding source code by automatically
+visualizing program structure. See example graphs:

 
 

+- [[https://www3.svjatoslav.eu/projects/sixth-3d/graphs/][Diagrams]] for [[https://www3.svjatoslav.eu/projects/sixth-3d/][Sixth 3D engine project]].
++ [[file:graphs/][Diagrams for JavaInspect project itself]].

 
 *A very simple example:*
 
 *A very simple example:*

-

 [[file:example.png][file:example-thumbnail.png]]
 
 Graph legend:
 file:legend.png
 
 [[file:example.png][file:example-thumbnail.png]]
 
 Graph legend:
 file:legend.png
 

+JavaInspect can be used as a [[file:Usage from CLI/][standalone commandline utility]] or as a
+[[file:Usage via Java API/][Java library]]. It uses Java's built-in reflection to discover and
+visualize any part of a Java program.

 
 

-+ [[https://www3.svjatoslav.eu/projects/sixth-3d/graphs/][See example produced graphs]] for [[https://www3.svjatoslav.eu/projects/sixth-3d/][Sixth 3D - 3D engine project]].
+See [[#usage][usage]] to learn how to use JavaInspect.
+
+After discovering application structure and optionally filtering out
+unimportant parts, JavaInspect produces a GraphViz DOT file describing
+the data to visualize. It then launches [[https://graphviz.org/][GraphViz]] to generate the
+graph image in PNG or SVG format.

 
 ** See also
 :PROPERTIES:
 
 ** See also
 :PROPERTIES:


@@ -58,20 +49,20 @@ Similar or alternative solutions:
 :PROPERTIES:
 :CUSTOM_ID: installation
 :END:
 :PROPERTIES:
 :CUSTOM_ID: installation
 :END:

-[[http://www.graphviz.org/][GraphViz]] - shall be installed on the computer.
+[[http://www.graphviz.org/][GraphViz]] must be installed on your system.

 
 

-On Ubuntu/Debian GraphViz can be installed using:
+On Ubuntu/Debian, install GraphViz using:

 #+BEGIN_SRC sh
 sudo apt-get install graphviz
 #+END_SRC
 
 To use JavaInspect via Java API, no further installation is
 needed. JavaInspect will be embedded into your project as dependency.
 #+BEGIN_SRC sh
 sudo apt-get install graphviz
 #+END_SRC
 
 To use JavaInspect via Java API, no further installation is
 needed. JavaInspect will be embedded into your project as dependency.

-This is described in [[id:bbeeffc8-3767-440d-8d93-ec9124dd60ee][usage via Java API]]. It will expect GraphViz to be
+This is described in [[file:Usage via Java API/][usage via Java API]]. It will expect GraphViz to be

 available in the system.
 
 To use JavaInspect as a commandline tool, JavaInspect source
 available in the system.
 
 To use JavaInspect as a commandline tool, JavaInspect source

-repository has to be cloned locally. See: [[id:c47ff9a6-d737-4b73-9393-1c63d2ca1101][Getting the source code]].
+repository has to be cloned locally. See: [[#getting-the-source-code][Getting the source code]].

 
 Then study and execute installation script:
 #+begin_src sh
 
 Then study and execute installation script:
 #+begin_src sh


@@ -87,137 +78,14 @@ Quick commandline usage help can be viewed by issuing
 
 * Usage
 :PROPERTIES:
 
 * Usage
 :PROPERTIES:

-:ID:       2ad2889e-6c95-4662-b3f4-2c341fc74522

 :CUSTOM_ID: usage
 :END:
 :CUSTOM_ID: usage
 :END:

-JavaInspect utility can be used in 2 different ways:
-+ [[id:acf1896a-74b4-4914-acf6-a77075e07f25][As standalone commandline utility]]
-+ [[id:bbeeffc8-3767-440d-8d93-ec9124dd60ee][As embedded Java library via Java API]]
-
-** Usage via Java API
-:PROPERTIES:
-:ID:       bbeeffc8-3767-440d-8d93-ec9124dd60ee
-:CUSTOM_ID: usage-via-java-api
-:END:
-Requires that classes to be visualised are available in the classpath.
-
-To get JavaInspect into same classpath with your projecs I so far came
-up with 2 solutions:
-
-1. Add JavaInspect library in your project as a dependency.
-
-2. Create new Java project for the purpose visualizing your other
-   projects and include JavaInspect and your projecs binary artifacts
-   (Jar's) into new project classpath. Built binary Jar's (with no
-   source code) are sufficient because JavaInspect operates via
-   reflection.
-
-Simple Java based control/configuration code needs to be written for
-each project. I usually put such code into directories devoted for
-JUnit tests. Because it needs not to be compiled/embedded into final
-product or project artifact I'm just willing to visualize.
-
-Control code in general does the following:
-1. Create graph object.
-2. Java reflection/classloaders does not provide mechanism for
-   discovering all classes under given package. Therefore you need to
-   declare at least some classes to be added to the graph by manually
-   adding individual classes to the graph. For every class added to
-   the graph, GraphViz will recursively inspect it and add all
-   referecned classes to the graph as well.
-3. Graphs easilly get very big and complex so optionally we filter
-   important code using classname [[https://en.wikipedia.org/wiki/Glob_(programming)][glob]] patterns based blacklist and/or
-   whitelist.
-4. Optionally we can tune some rendering parameters like:
-   + Possibility to remove orphaned classes (classes with no
-     references) from the graph.
-   + Specify target directory for generated visualization
-     files. (Default is current directory)
-   + Keep intermediate GraphViz dot file for later inspection.
-5. Render graph.
-
-
-*** Example 1: individually picked objects
-:PROPERTIES:
-:CUSTOM_ID: example-1-individually-picked-objects
-:END:
-This example demonstrates generating of class graph from hand picked
-classes and visualizing GraphViz itself.
-
-#+BEGIN_SRC java
-
-// Create graph
-final ClassGraph graph = new ClassGraph();
-
-// Add some random object to the graph. GraphViz will detect Class from
-// the object.
-graph.add(graph);
-
-// Also add some random class to the graph.
-graph.add(Utils.class);
-
-// Keep intermediary GraphViz DOT file for reference.
-graph.setKeepDotFile(true);
-
-// Produce bitmap image titled "JavaInspect.png" to the user Desktop
-// directory
-graph.generateGraph("JavaInspect");
-
-#+END_SRC
-
-Note: if desired, more compact version of the above:
-#+BEGIN_SRC java
-new ClassGraph().add(randomObject, RandomClass.class)
-                .setKeepDotFile(true).generateGraph("JavaInspect");
-#+END_SRC
-
-
-Result:
-    - Generated DOT file: [[file:JavaInspect.dot][JavaInspect.dot]]
-    - Generated PNG image: [[file:JavaInspect.png][JavaInspect.png]]
-
-*** Example 2: GraphViz embedded in another project
-:PROPERTIES:
-:CUSTOM_ID: example-2-graphviz-embedded-in-another-project
-:END:
-1. Download project Sixth [[https://www2.svjatoslav.eu/gitweb/?p=sixth.git;a=snapshot;h=HEAD;sf=tgz][code snapshot]].
-2. Inspect and run *DataGraph.java*.
-
-*** Embedding JavaInspect in your Maven project
-:PROPERTIES:
-:CUSTOM_ID: embedding-javainspect-in-your-maven-project
-:END:
-
-Declare JavaInspect as dependency:
-#+BEGIN_SRC xml
-<dependencies>
-    ...
-    <dependency>
-        <groupId>eu.svjatoslav</groupId>
-        <artifactId>javainspect</artifactId>
-        <version>1.7</version>
-    </dependency>
-    ...
-</dependencies>
-#+END_SRC
-
-
-Add Maven repository to retrieve artifact from:
-#+BEGIN_SRC xml
-<repositories>
-    ...
-    <repository>
-        <id>svjatoslav.eu</id>
-        <name>Svjatoslav repository</name>
-        <url>https://www3.svjatoslav.eu/maven/</url>
-    </repository>
-    ...
-</repositories>
-#+END_SRC
+JavaInspect can be used in two ways:
++ [[file:Usage from CLI/][As a standalone commandline utility]]
++ [[file:Usage via Java API/][As a Java library embedded in your project]]

 
 * Source code
 :PROPERTIES:
 
 * Source code
 :PROPERTIES:

-:ID:       c47ff9a6-d737-4b73-9393-1c63d2ca1101

 :CUSTOM_ID: getting-the-source-code
 :END:
 
 :CUSTOM_ID: getting-the-source-code
 :END:
 

diff --git a/doc/upsage from cli/index.org b/doc/upsage from cli/index.org
deleted file mode 100644 (file)
index 91ec55e..0000000
--- a/doc/upsage from cli/index.org
+++ /dev/null
@@ -1,112 +0,0 @@
-:PROPERTIES:
-:ID:       acf1896a-74b4-4914-acf6-a77075e07f25
-:END:
-#+SETUPFILE: ~/.emacs.d/org-styles/html/darksun.theme
-#+TITLE: JavaInspect - usage from commandline
-#+LANGUAGE: en
-#+LATEX_HEADER: \usepackage[margin=1.0in]{geometry}
-#+LATEX_HEADER: \usepackage{parskip}
-#+LATEX_HEADER: \usepackage[none]{hyphenat}
-
-#+OPTIONS: H:20 num:20
-#+OPTIONS: author:nil
-
-[[file:../index.org][Back to main documentation]]
-
-* Commandline arguments
-:PROPERTIES:
-:CUSTOM_ID: available-commandline-arguments
-:END:
-
-
-- -j (existing files)... :: JAR file(s) to render.
-
-- -c (existing directories)... :: Classpath directories
-
-- -n (string) :: Graph name. (default: "graph")
-
-- --debug :: Show debug info.
-
-- -h, --help :: Show commandline usage help.
-
-- -k :: Keep dot file.
-
-- -ho ::
-    Hide orphaned classes.
-
-- -w (one to many strings)... :: Whitelist glob(s).
-
-- -b (one to many strings)... :: Blacklist glob(s).
-
-- -r (one to many strings)... :: root class(es).
-
-- -d (existing directory) :: Target directory. Default is current directory.
-
-- -t (options: png, svg) :: Target image type. Default is: svg.
-
-* Specifying classes to render
-:PROPERTIES:
-:CUSTOM_ID: specifying-classes-to-render
-:END:
-
-Normal Java application has immense complexity. In addition to code
-that was directly written by particular project developers, lots of
-functionality is typically added as frameworks or libraries to the
-project. In addition there is significant Java standard library.
-
-Because JavaInspect uses reflection, it does not easily distinguish
-between those. In normal situation you would rather want to visualize
-only code that was developed specifically for your project and leave
-frameworks like Spring etc. out. If you visualize all classes that are
-possibly reachable from you project, you will easily get huge and
-incomprehensible graph.
-
-JavaInspect can digest compiled Java classes in 2 modes:
-1. Provide list of Jar files. Use *-j* option.
-2. Provide list of filesystem directories that can be used as
-   classpath root. Use *-c* option.
-
-Currently JavaInspect uses following algorithm to add classes to
-rendered graph:
-
-- All classes that were found in Jar files are added to graph by default.
-- None of the classes that were found in filesystem directories are
-  added to the graph by default (unless explicitly referenced). (TODO:
-  for consistency it would be better to add them too by default)
-- If whitelist is specified (*-w* option) everything that is not
-  matched by whitelist pattern(s) will be removed from the graph.
-- If blacklist is specified (*-b* option) everything that is matched
-  by blacklist pattern(s) will be removed from the graph.
-- Root classes can be specified using *-r* option. Root classes will
-  be added to the graph. JavaInspect will then try to recursively
-  discover all classes that were referenced by root class and add
-  those also to the graph.
-
-* Examples
-:PROPERTIES:
-:CUSTOM_ID: examples
-:END:
-
-Visualize java Jar file. All classes. Hide orphaned classes:
-
-#+begin_src sh
-  javainspect \
-      -j target/sixth-3d-*-SNAPSHOT.jar \
-      -d doc/graphs/ \
-      -n "all classes" \
-      -t png -ho
-#+end_src
-
-
-Visualize java Jar file. All classes. Hide orphaned classes. Apply
-whitelist:
-
-#+begin_src sh
-  javainspect \
-      -j target/sixth-3d-*-SNAPSHOT.jar \
-      -d doc/graphs/ \
-      -n "GUI" \
-      -t png \
-      -w "eu.svjatoslav.sixth.e3d.gui.*" \
-      -ho
-#+end_src