refactor: Remove AnnotatedDocument class

The AnnotatedDocument class was, essentially, a simple tuple of a document
and a list of annotations. While not bad in a vacuum, it is unwieldy and
passing this around instead of a document, annotations, or both where
necessary is more restrictive and frankly unnecessary.

This commit removes the data class and any instances of its use. Instead,
we now pass the individual components around to anything that needs them.
This also frees us up to pass only annotations around for example.

We also do not iterate through the selected papis documents to work on
in each exporter anymore (since we only pass a single document), but
in the main function itself. This leads to less duplication and makes
the overall run function the overall single source of iteration through
selected documents. Everything else only knows about a single document -
the one it is operating on - which seems much neater.

For now, it does not change much, but should make later work on extra
exporters or extractors easier.

papis_extract/exporter.py

@@ -6,27 +6,33 @@ import papis.api
 import papis.git
 import papis.config
 import Levenshtein
-from papis_extract.annotation import AnnotatedDocument
+from papis_extract.annotation import Annotation
 
 from papis_extract.formatter import Formatter
 
 logger = papis.logging.get_logger(__name__)
 
 
-def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None:
+def to_stdout(
+    formatter: Formatter,
+    document: papis.document.Document,
+    annotations: list[Annotation],
+) -> None:
     """Pretty print annotations to stdout.
 
     Gives a nice human-readable representations of
     the annotations in somewhat of a list form.
     Not intended for machine-readability.
     """
-    output: str = formatter(annotated_docs)
-    print(output.rstrip("\n"))
+    output: str = formatter(document, annotations)
+    if output:
+        print(output.rstrip("\n"))
 
 
 def to_notes(
     formatter: Formatter,
-    annotated_docs: list[AnnotatedDocument],
+    document: papis.document.Document,
+    annotations: list[Annotation],
     edit: bool,
     git: bool,
     force: bool,
@@ -37,13 +43,12 @@ def to_notes(
     belonging to papis documents. Creates new notes for
     documents missing a note field or appends to existing.
     """
-    for entry in annotated_docs:
-        formatted_annotations = formatter([entry]).split("\n")
-        if formatted_annotations:
-            _add_annots_to_note(entry.document, formatted_annotations, force=force)
+    formatted_annotations = formatter(document, annotations).split("\n")
+    if formatted_annotations:
+        _add_annots_to_note(document, formatted_annotations, force=force)
 
-        if edit:
-            papis.commands.edit.edit_notes(entry.document, git=git)
+    if edit:
+        papis.commands.edit.edit_notes(document, git=git)
 
 
 def _add_annots_to_note(