21. In a computer-implemented system for providing annotated electronic documents, the annotations which are to be applied to the documents being stored in a first data storage, the documents being stored in a second data storage, a method for annotating documents, implemented by a computer system, said method comprising the at least one of sequential, non-sequential and sequence-independent steps of: (A) determining, in the computer system and responsive to a user, at least one annotation to be applied to at least one document, including selecting at least a portion of the at least one document to be annotated, associating the at least one annotation with the at least one portion, and editing the at least one annotation associated with the at least one portion, wherein the annotation is image data or text, wherein each annotation can be different from every other annotation; and (B) responsive to a user, at least one of establishing, traversing, indicating, and removing at least one reference from the at least one portion to at least one of an other portion of the at least one document, an other document, and at least one other portion of the other document; and (C) by a merge component of the computer system, responsive to a request from the user to retrieve the at least one document, retrieving the at least one document from a second data storage as document data, retrieving the at least one annotation to be applied to said at least one document from a first data storage as annotation data, and combining the annotation data and the document data to form a unitary single logical document, the single logical document displaying the annotation embedded seamlessly in the document data, (D) by at least one split component of the computer system, the split component being complementary to the merge component, responsive to a request from the user to store the document: extracting the annotation data and the document data from the single logical document, updating the at least one annotation in the first data storage from the extracted annotation data, and updating the at least one document in the second data storage from the extracted document data, wherein the annotation data indicates a predetermined section within the document as stored in the second data storage into which the annotation is to be embedded as indicated by an XML data schema.
21. In a computer-implemented system for providing annotated electronic documents, the annotations which are to be applied to the documents being stored in a first data storage, the documents being stored in a second data storage, a method for annotating documents, implemented by a computer system, said method comprising the at least one of sequential, non-sequential and sequence-independent steps of: (A) determining, in the computer system and responsive to a user, at least one annotation to be applied to at least one document, including selecting at least a portion of the at least one document to be annotated, associating the at least one annotation with the at least one portion, and editing the at least one annotation associated with the at least one portion, wherein the annotation is image data or text, wherein each annotation can be different from every other annotation; and (B) responsive to a user, at least one of establishing, traversing, indicating, and removing at least one reference from the at least one portion to at least one of an other portion of the at least one document, an other document, and at least one other portion of the other document; and (C) by a merge component of the computer system, responsive to a request from the user to retrieve the at least one document, retrieving the at least one document from a second data storage as document data, retrieving the at least one annotation to be applied to said at least one document from a first data storage as annotation data, and combining the annotation data and the document data to form a unitary single logical document, the single logical document displaying the annotation embedded seamlessly in the document data, (D) by at least one split component of the computer system, the split component being complementary to the merge component, responsive to a request from the user to store the document: extracting the annotation data and the document data from the single logical document, updating the at least one annotation in the first data storage from the extracted annotation data, and updating the at least one document in the second data storage from the extracted document data, wherein the annotation data indicates a predetermined section within the document as stored in the second data storage into which the annotation is to be embedded as indicated by an XML data schema. 22. The method of claim 21 , further comprising: providing, from the single logical document, a report listing each annotation in the at least one document, and in visual correspondence thereto a summary of each portion in the at least one document that is associated with each annotation; and providing a map listing a summary of each portion in the at least one document, each annotation in the at least one document including the at least one annotation, and each reference from the at least one portion of the document, including the at least one reference, wherein each annotation and each reference is visually linked to a corresponding portion listed in the summary.