fixing paper build

Makefile

@@ -253,8 +253,8 @@ test:
 count-lines:
 	@$(NX) run research:stats
 
-all:
-	@$(NX) run paper:build
+# Default artifact set for this repo: thesis PDF (same as pdf).
+all: pdf
 
 .PHONY: manim.defense manim.defense.hq manim.render manim.render.full manim.render.poster manim.render.appendix manim.render.all
 # Main defense reel (paper/defense/manim/render_defense); uses paper/defense/.venv when present

paper/.latexmkrc

@@ -4,5 +4,23 @@ $bibtex_use = 2;                       # run biber when biblatex .bcf changes
 # biber cwd is paper/build; scripts/nx_paper.sh symlinks ../build/bib -> ../src/bib so
 # datasources log as bib/references.bib and latexmk's -e check works from paper/src
 $biber    = 'biber %O %S';
+
+# Stale latexmk db: biblatex uses biber + .bcf, but the fdb can keep a "bibtex" rule after a bad
+# run. Then biber never runs and citations stay undefined. Read whole fdb (small) so the rule
+# line is never missed after a long dependency list.
+for my $job (qw(main main-genpop summary)) {
+    my $bcf = "../build/$job.bcf";
+    my $bbl = "../build/$job.bbl";
+    my $fdb = "../build/$job.fdb_latexmk";
+    next unless -e $fdb && -e $bcf;
+    my $drop = !-e $bbl;
+    if ( !$drop && open my $fh, '<', $fdb ) {
+        local $/;
+        my $body = <$fh>;
+        close $fh;
+        $drop = 1 if defined $body && $body =~ /\["bibtex $job"\]/;
+    }
+    unlink $fdb if $drop;
+}
 $pdf_previewer = 'zathura %O %S';
 $clean_ext = 'synctex.gz bbl bcf run.xml fls fdb_latexmk glg glo gls ist blg lof lot out toc';

scripts/nx_paper.sh

@@ -27,18 +27,17 @@ link_build_bib() {
   ln -sfn ../src/bib ../build/bib
 }
 
-# latexmk can exit non-zero with "biber ... gave an error in previous invocation" while the PDF is
-# already fine: incremental runs skip biber but keep a stale failure bit in main.fdb_latexmk.
-# One forced cycle (-g) re-runs biber and clears that state.
-latexmk_paper() {
-  local job="$1"
-  local tex="$2"
-  local -a common
-  common=( -pdf -jobname="$job" -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build )
-  latexmk "${common[@]}" "$tex" || {
-    printf '%s\n' "latexmk failed; retrying once with -g (clear stale biber/latexmk state)" >&2
-    latexmk -g "${common[@]}" "$tex"
-  }
+# Biblatex uses biber; a stale latexmk fdb can still record ["bibtex <job>"], so latexmk skips
+# biber, main.bbl is missing or wrong, and every citation stays undefined. Drop only that case.
+drop_stale_latexmk_bibtex_fdb() {
+  local job fdb tag
+  for job in main main-genpop summary; do
+    fdb="../build/${job}.fdb_latexmk"
+    tag=$(printf '["bibtex %s"]' "$job")
+    if [[ -f "$fdb" ]] && grep -Fq "$tag" "$fdb"; then
+      rm -f "$fdb"
+    fi
+  done
 }
 
 case "$cmd" in
@@ -48,13 +47,15 @@ case "$cmd" in
     bash paper/concat_code.sh
     cd paper/src
     link_build_bib
-    latexmk_paper main main.tex
+    drop_stale_latexmk_bibtex_fdb
+    latexmk -pdf -jobname=main -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build main.tex
     ;;
   watch)
     mkdir -p paper/build
     sync_mdp_figures
     cd paper/src
     link_build_bib
+    drop_stale_latexmk_bibtex_fdb
     latexmk -pvc -pdf -jobname=main -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build main.tex
     ;;
   clean)
@@ -77,13 +78,15 @@ case "$cmd" in
     sync_mdp_figures
     cd paper/src
     link_build_bib
-    latexmk_paper main-genpop main-genpop.tex
+    drop_stale_latexmk_bibtex_fdb
+    latexmk -pdf -jobname=main-genpop -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build main-genpop.tex
     ;;
   watch-genpop)
     mkdir -p paper/build
     sync_mdp_figures
     cd paper/src
     link_build_bib
+    drop_stale_latexmk_bibtex_fdb
     latexmk -pvc -pdf -jobname=main-genpop -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build main-genpop.tex
     ;;
   build-arxiv)
@@ -99,12 +102,14 @@ case "$cmd" in
     mkdir -p paper/build
     cd paper/src
     link_build_bib
-    latexmk_paper summary summary.tex
+    drop_stale_latexmk_bibtex_fdb
+    latexmk -pdf -jobname=summary -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build summary.tex
     ;;
   watch-summary)
     mkdir -p paper/build
     cd paper/src
     link_build_bib
+    drop_stale_latexmk_bibtex_fdb
     latexmk -pvc -pdf -jobname=summary -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build summary.tex
     ;;
   *)