[wip] ai-revision: update config files with current prompts

content/ai_revision-config.yaml

@@ -2,3 +2,7 @@ files:
   ignore:
     - front\-matter
     - back\-matter
+  matchings:
+    - files:
+        - .*\.md$
+      prompt: default

content/ai_revision-prompts.yaml

@@ -1,3 +1,43 @@
-prompts_files:
-  \.md$: |
-    Proofread the following paragraph
+prompts:
+  abstract: |
+    You are a scientist with copy-editing skills who will help in improving the
+    text of a manuscript. Revise the following abstract of this manuscript so
+    that it has a clear sentence structure and fits in a single paragraph. The
+    revision should follow a context-content-conclusion (C-C-C) scheme, as
+    follows: 1) The context portion communicates to the reader what gap the
+    paper will fill. The first sentence orients the reader by introducing the
+    broader field in which the manuscript's research is situated. Then, the
+    context is narrowed until it lands on the open question that the research
+    answers. A successful context section distinguishes the research's
+    contributions from the current state-of-the-art, communicating what is
+    missing in the current literature (i.e., the specific gap) and why that
+    matters (i.e. the connection between the specific gap and the broader
+    context). 2) The content portion (e.g. "here we") first describes the novel
+    method or approach that was used to fill the gap, then presents an executive
+    summary of results. 3) The conclusion portion interprets the results to
+    answer the question that was posed at the end of the context portion. There
+    may be a second part to the conclusion portion that highlights how this
+    conclusion moves the broader field forward (e.g. "broader significance").
+
+  introduction: |
+    You are a scientist with copy-editing skills tasked with refining the text
+    of a scientific manuscript. Your goal is to revise the following paragraph
+    from the Introduction section to enhance clarity, reduce jargon, and
+    maintain a scholarly tone. The revision should adhere to Markdown formatting
+    and follow a Context-Content-Conclusion (C-C-C) structure. This structure
+    begins by setting the stage with one or two sentences (Context), progresses
+    through what is known from the literature (Content), and concludes by
+    highlighting an aspect of the knowledge gap the manuscript addresses
+    (Conclusion). Your revision should: 1) preserve the original information as
+    much as possible, with minimal changes to the text, 2) ensure most
+    references to scientific articles are kept exactly as they appear in the
+    original text; these references are crucial for academic integrity and may
+    appear with the format "[@TYPE:ID]" such as "[@pmid:33931583;
+    @doi:10.1101/2021.10.21.21265225; @pmid:31036433]", and 4) the revised
+    paragraph must encapsulate the entire revision, following the C-C-C
+    structure, within a single, cohesive paragraph.
+
+  default: |
+    Proofread the following paragraph that is part of a scientific manuscript.
+    Keep all Markdown formatting, citations to other articles, mathematical
+    expressions, and equations.