Wire up references.bib and verify citations against source PDFs ...

- Add citations/ folder holding the cited papers' PDFs (babapoor2022,
  wu2011, nishi2021), documented in CLAUDE.md so cite keys can be
  filled in/verified directly from the source paper instead of guessed.
- Fill in references.bib entries for all three keys with real
  bibliographic data, and drop a stray "@TODO" in the header comment
  that was making bibtex misparse the file as a malformed entry.
- Switch main.tex from the template's placeholder internal
  bibliography to \bibliography{references}, so citations actually
  resolve (previously rendered as undefined/"?").
- Correct the Introduction's babapoor2022/wu2011 citation claims after
  reading the full papers: babapoor2022 reports separate no-reflow
  (17.1%) and slow-flow (12.9%) rates in a single-center primary-PCI
  cohort, not a general "10-20% of PCI patients" figure; wu2011's
  finding is specific to AMI patients and a composite no-reflow/
  slow-flow (TIMI <=2) endpoint, and only the amount (not presence) of
  attenuated plaque differed significantly.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Draft Introduction via ja-drafter/review/translate pipeline ...

Writes sections/1_introduction.tex through the documented workflow:
Japanese draft (drafts/ja/1_introduction.md), fact-check + content
review against the Notion source of truth, then English translation.
Centers the section on the proposed KSCNet architecture; open claims
without a source yet are left as inline [citation needed] markers.
Also documents the pipeline itself in CLAUDE.md.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Number section files to match reading order ...

sections/*.tex renamed to 1_introduction.tex .. 6_conclusion.tex so the
directory listing sorts in the same order they're \input from main.tex.
No 0_abstract.tex: the abstract must stay inline in main.tex (mdpi.cls
reuses it as PDF pdfsubject metadata, which \input breaks), and a
drafting-only file would just duplicate it with a risk of drifting out
of sync, so CLAUDE.md now says so explicitly.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

CLAUDE.md: add drafting/translation conventions ...

- Don't fill gaps with unstated inference; ask when something needed
  for the manuscript is unclear or unspecified.
- Translate Japanese source material faithfully, not as a loose
  paraphrase, while still producing natural English.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Split manuscript body into main.tex + sections/, move template to Template/ ...

main.tex is now the actual manuscript to edit and compile, copied from
the official MDPI template. Body content moves out into
sections/{introduction,related_work,method,experiment,discussion,
conclusion}.tex, \input from main.tex right after each \section heading;
figures/ added for images. Abstract stays inline in main.tex since
mdpi.cls reuses it verbatim as PDF pdfsubject metadata, which requires
full expandability that \input breaks.

The pristine template (template.tex/template.pdf) moves into its own
Template/ folder to stay visually distinct from the actual manuscript;
its \documentclass/\includegraphics calls are updated to ../Definitions/
accordingly. It's kept as read-only reference going forward.

Also removes the template's "How to Use this Template" placeholder
section and the unused optional Patents section, and documents the new
layout in CLAUDE.md.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Correct CLAUDE.md: TeX Live 2026 is installed on WSL, just not on PATH for non-interactive shells ...

Verified by compiling template.tex via an interactive zsh shell.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Set up Claude Code environment for the MDPI manuscript ...

- Add CLAUDE.md documenting project context, source-material timeline
  and caveats, manuscript structure, and Windows/WSL/macOS environment
  notes.
- Add references.bib stub seeded with cite keys from the MIDL paper.
- Untrack *:Zone.Identifier marker files and ignore them going forward,
  along with common LaTeX build artifacts.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>