Alpha fixes (#4)

* Fix start up text error and edit read me file.

* More README.md editing.

* More README.md editing.

* More README.md editing.

* More README.md editing.

* Fix an syntax mistake

README.md

@@ -1,5 +1,147 @@
 # JWriter
-This is a writing software foucsed on writing for both fiction and non-fiction. It is simpiler to project like [FoucsWriter](https://gottcode.org/focuswriter/). This project is currently in alpha version, and will be optimized and will have more features.
-Screen shots:
+
+## About
+JWriter a word processor with note taking and goal setting ablities. It is
+foused for authors to write fiction and non-fiction alike.  Notes can be put
+into to the file anywhere yet allow easy to navigate to them. The goal settings
+can be adjest as the document written.
+
+Even though the markup language is made for this program, is very forgiving and
+will highlight the syntax. In the future, there will be more support and will
+have a [WYSIWYG mode](https://en.wikipedia.org/wiki/WYSIWYG). This make learning
+the language as just a faster way to format and insert notes and agendas.
+
+This project is currently in alpha version, and will be optimized and will have
+more features.
+
+## Markup
+
+### Formats
+There are four different formats. Formats can be combined, but are only restrict
+to one line.
+
+|Format   |Code          |
+|---------|--------------|
+|Italics  |`\*Text\*`    |
+|Bold     |`\*\*Text\*\*`|
+|Underline|`\_Text\_`    |
+|Code     |`\`Text\``    |
+
+There are also [footnote (syntax `{^footnote}`), endnote (syntax `{*endnote}`)](#note-styles),
+[links (syntax `<@reference id|link text>` or `<link path|link text>`)](#hyperlink),
+[agenda (syntax `{! todo}`)](#agenda), and [citation (sytnax `{@id}`)](#notes).
+
+## Sections
+Each section had a heading or an outline point at the top of the section. This
+markup language allows you to have no heading or outline, but the section has to
+be at the top of file. An outline point is nested inside a section with an
+heading, or is before the first section with headings.
+
+
+### Heading and outline
+
+A heading or an outline can have an [id](#id) that can be linked to a
+different point of file.  The syntax is `@category-id:` and it set before the
+first text, other than the syntax used to indicated the heading and outline
+style. Refers to the section by using [`<@id>`](#hyperlink).
+
+There are six level for both headings and outlines.
+
+A heading or an outline can also have a status with details, A status is
+optional, and can be `#STUB`, `#DRAFT`, `#FINAL`, `#` (custom) and none. after
+the status, there are details to go with the status. It will be at the end of
+the line.
+
+The syntax of a heading is:
+
+    = @category-id:Title for largest heading # status
+    == Title for heading 2 #DRAFT
+    ======Smallest headings
+
+The syntax of a outline is:
+
+    !# Largest outline point
+    !######Smallest outline pointe
+
+
+### Main Line Styles
+
+There are several types of line styles.
+
+|Line styles  |Syntax    |Notes                                                |
+|-------------|----------|-----------------------------------------------------|
+|Numbered     | `# text` |Add tabs before `#` to increse level (up to six)     |
+|Bullet       | `- text` |Add tabs before `-` to increse level (up to six)     |
+|Quote        | `> text` |                                                     |
+|Section Break| `***`    |It has no text after the `*` or allow spaces anywhere|
+|Paragaph     | `text`   |There is no symbol used at the beginning of the line |
+
+### Note Styles
+In addition there are footnote, and endnote, that can be referred to even
+outside of the section that the line belongs in. Footnotes appears at end of a
+page, while endnote appears at the end of either a section or a document.
+
+All footnote and endnotes will have an [id](#id) and text before they can appear
+in the printed document.
+
+|Types      |Line Syntax |In Text Syntax|
+|-----------|------------|--------------|
+|Footnote   | `!^id:text`| `{^id}`      |
+|Endnote    | `!*id:text`| `{*id}`      |
+
+Footnote will count by numbers, while endnot count by letters.
+
+### Hyperlink
+
+Hyperlinks can be link to a section or a webpage. If the referred link points to
+
+A referred link needs a line somewhere with the following syntax:
+
+    !@id:webpage path
+
+A referred link needs to have an [id](#id) and text before it can appears in the
+printed document.
+
+Both referred link and section links has the following sytnax: `<@id|text>` while
+direct links has the following syntax: `<web page path| text>`. Text (include the
+symbol `|` are optional, and will be replace by the web page path or the section
+title if none is found.
+
+### Agenda
+Agenda marks parts of the document to be work on later. There are two types of
+agendas, in text or a single line.
+
+In text agenda uses the following syntax `{@text}` while a single line of agenda
+uses the following syntax:
+
+    !! to do text
+
+## Notes
+
+Note has the following syntax:
+
+    !% @id: text
+    !% more text
+    !>source: sources
+
+[Id](#id) and sources are optional, but both are required if the note is from
+research and is being use as a citation.
+
+Sources has requires two things:
+
+- a line of formated text to appear in the word cited section at the end of
+  document or section which starts with `!>source:`
+- a way to cite in text with start the line with one of the following:
+    - `!>in-text:` appears in the text
+    - `!>footnote:` appears as a footnote
+
+## Id
+
+Ids have an category and title. There are unlimited number of categories and
+unlimited of nested subcategories avaiable. the categories and titles are sorted
+in the alphabethical order and are not case sensitive. The syntax of an id is
+`category-subcategory-...-title`.
+
+## Screen shots
 ![Main Window](design/main.png)
 ![Stats Window](design/stats.png)

src/com/creativeartie/jwriter/file/ManuscriptFile.java

@@ -54,20 +54,14 @@ public static ManuscriptFile newFile() {
             new RecordTable());
     }
 
-    private ManuscriptFile(File file, ManuscriptDocument doc,
+    public ManuscriptFile(File file, ManuscriptDocument doc,
         RecordTable table)
     {
         zipFile = Optional.ofNullable(file);
         documentText = doc;
         recordsFile = table;
     }
 
-    public ManuscriptFile(File doc) throws IOException{
-        zipFile = Optional.empty();
-        documentText = new ManuscriptDocument(doc);
-        recordsFile = new RecordTable();
-    }
-
     public void setSave(File file){
         zipFile = Optional.of(file);
     }

src/com/creativeartie/jwriter/main/Main.java

@@ -29,24 +29,26 @@ public void start(Stage stage) throws Exception{
         stage.setTitle(TEXTS.getString("MainWindow.Title"));
 
         // testStatsWindow(stage);
-        // testMainWindow(stage);
-        jarMainWindow(stage);
+        openMainWindow(stage);
     }
 
-    private void testMainWindow(Stage stage) throws Exception{
-        setupWindow(stage, new File("data/help-text.txt"));
+    private void openMainWindow(Stage stage) throws Exception{
+        ClassLoader classLoader = getClass().getClassLoader();
+        InputStream in = getClass().getResourceAsStream("/data/help-text.txt");
+        StringBuilder builder = new StringBuilder();
+        int read = in.read();
+        while (read != -1){
+            builder.append((char) read);
+            read = in.read();
+        }
+        setupWindow(stage, new ManuscriptFile(null,
+            new ManuscriptDocument(builder.toString()), new RecordTable()));
     }
 
-    private void jarMainWindow(Stage stage) throws Exception{
-        File classPath = new File(System.getProperty("java.class.path"));
-        File file = new File(classPath.getParent(), "data/help-text.txt");
-        setupWindow(stage, file);
-    }
-
-    private void setupWindow(Stage stage, File file) throws Exception{
+    private void setupWindow(Stage stage, ManuscriptFile file) {
         SceneWriterControl writer = new SceneWriterControl(stage);
         Scene scene = new Scene(writer, 800, 600);
-        writer.setManuscriptFile(new ManuscriptFile(file));
+        writer.setManuscriptFile(file);
         stage.setScene(scene);
         stage.setMaximized(true);
         stage.show();