thesis-progress

Context

Options: $ARGUMENTS

Today: !date +%Y-%m-%d

Chapter files:

!ls chapters/*.tex chapters/*.md 2>/dev/null || echo "(no chapters directory)"

Raw word counts (markup included; refine below):

!wc -w chapters/*.tex chapters/*.md 2>/dev/null | tail -20

Placeholders:

!grep -rn --include='*.tex' --include='*.md' -E '\[\[(FILL|CITE|FIG|TODO)[^]]*\]\]' chapters 2>/dev/null | wc -l | xargs -I{} echo "{} placeholders"

Reading:

!echo "notes: $(ls research/notes 2>/dev/null | wc -l | tr -d ' '), reading list entries: $(grep -c '^## ' research/reading-list.md 2>/dev/null || echo 0)"

Research log:

!grep -c '^## ' RESEARCH_LOG.md 2>/dev/null | xargs -I{} echo "{} entries"; awk '/^### Open/{f=1;next} /^###|^## /{f=0} f' RESEARCH_LOG.md 2>/dev/null | head -10

Recent activity:

!git log --since='14 days ago' --format=' %ad %s' --date=short 2>/dev/null | head -15

Task

Produce a one-screen status report. Numbers, not adjectives.

Word counts

Use texcount -inc -total -brief for LaTeX or pandoc file -t plain | wc -w for Markdown so markup is excluded. Compare each chapter against its target from the chapter plan (proposal, research/OUTLINE.md, or --target-words split evenly). Show a table: chapter, words, target, percent, placeholders.

Citation health

Count unique cite keys across chapters, keys not in the .bib, and .bib entries with no doi/eprint/url. If research/citation-report.md exists, show its date and totals; if it is older than the newest chapter edit, say a rerun of citation-verifier is due.

Reading

Notes written versus reading-list entries; list entries with no note as the reading backlog (cap at 10).

Open items

The "Open" bullets from the last three log entries, with the age of each (from the entry date). Anything older than 14 days is flagged for the supervisor.

Time

Days to --deadline (or a deadline found in the proposal or research/QUESTION.md). Words remaining divided by days remaining gives the required daily rate; state it, and compare with the actual rate from git history over the last 14 days (words added per day, from git diff --shortstat).