8. An annotation handling computing system for processing annotations added to a base document, the annotation handling computing system comprising: one or more processors; memory communicatively coupled to the one or more processors, the memory having stored instructions that, when executed at the annotation handling computing system, configure the annotation handling computing system to implement: a parse engine configured to classify an element added to the base document to provide a parsed output result, the elements including a stroke or a group of strokes, the stroke being an individual mark created by a user on the base document by using a digitized tablet or like mechanism; a document layout analysis engine configured to analyze a layout of the base document to output a result of a determination of a composition of the base document, including image content, line content, or word content; an annotation engine comprising two or more sub-annotation engines for processing specific respective types of annotations, the annotations being represented by the strokes input by the user to mark supplemental information onto a portion of the base document, the annotation engine module configured to: receive the parsed output result as input from the core parser engine; receive the result from the document layout analysis engine; classify, by the two or more sub-annotation engines, one or more annotations added to the base document based on the parsed output result of the core parser engine and the result of the document layout analysis engine, each sub-annotation engine producing an annotation result that classified the annotation into a prescribed type and anchoring information that associates the annotation with other contents in the base document, the anchoring information being information that links the annotation to a specific content in the base document, the annotation result of one sub-annotation engine being provided to another sub-annotation engine such that the another sub-annotation engine is capable to obtain benefits from the annotation result of the one sub-annotation engine; and generate an output that represents a result of the automatic classification of annotations, the output comprising a hierarchical tree of annotations independent of the parsed out result from the core parser engine, the hierarchical tree of annotations identifying different classified types of annotations using different respective types of nodes; a reflow engine configured to use the generated output of the annotation engine to track the position of the annotations in the base document and to adjust the position of the annotation to continue to display the annotations in proper positional proximity to other contents of the base document; and one or more annotation-based application configured to use a result produced by the annotation engine and the reflow engine.
8. An annotation handling computing system for processing annotations added to a base document, the annotation handling computing system comprising: one or more processors; memory communicatively coupled to the one or more processors, the memory having stored instructions that, when executed at the annotation handling computing system, configure the annotation handling computing system to implement: a parse engine configured to classify an element added to the base document to provide a parsed output result, the elements including a stroke or a group of strokes, the stroke being an individual mark created by a user on the base document by using a digitized tablet or like mechanism; a document layout analysis engine configured to analyze a layout of the base document to output a result of a determination of a composition of the base document, including image content, line content, or word content; an annotation engine comprising two or more sub-annotation engines for processing specific respective types of annotations, the annotations being represented by the strokes input by the user to mark supplemental information onto a portion of the base document, the annotation engine module configured to: receive the parsed output result as input from the core parser engine; receive the result from the document layout analysis engine; classify, by the two or more sub-annotation engines, one or more annotations added to the base document based on the parsed output result of the core parser engine and the result of the document layout analysis engine, each sub-annotation engine producing an annotation result that classified the annotation into a prescribed type and anchoring information that associates the annotation with other contents in the base document, the anchoring information being information that links the annotation to a specific content in the base document, the annotation result of one sub-annotation engine being provided to another sub-annotation engine such that the another sub-annotation engine is capable to obtain benefits from the annotation result of the one sub-annotation engine; and generate an output that represents a result of the automatic classification of annotations, the output comprising a hierarchical tree of annotations independent of the parsed out result from the core parser engine, the hierarchical tree of annotations identifying different classified types of annotations using different respective types of nodes; a reflow engine configured to use the generated output of the annotation engine to track the position of the annotations in the base document and to adjust the position of the annotation to continue to display the annotations in proper positional proximity to other contents of the base document; and one or more annotation-based application configured to use a result produced by the annotation engine and the reflow engine. 11. The annotation handling computing system of claim 8 , wherein said two or more sub-annotation engines are selected from a group consisting of: a highlight annotation engine; an enclosing-type annotation engine; an underline annotation engine; a vertical bracket annotation engine; a call-out annotation engine; and a free-note annotation engine.