From 6427ae63ec4416006898e1577e8c81462b490d4a Mon Sep 17 00:00:00 2001
From: Daniel Rosel <daniel@alves.world>
Date: Fri, 10 Apr 2026 08:30:48 +0200
Subject: [PATCH] fixing paper build

---
 Makefile                         |   4 ++--
 paper/.latexmkrc                 |  18 ++++++++++++++++
 paper/src/chapters/mdp_agent.pdf | Bin 10932 -> 10931 bytes
 paper/src/chapters/mdp_human.pdf | Bin 11953 -> 11953 bytes
 scripts/nx_paper.sh              |  35 ++++++++++++++++++-------------
 5 files changed, 40 insertions(+), 17 deletions(-)

diff --git a/Makefile b/Makefile
index 315651e..cc9711f 100644
--- a/Makefile
+++ b/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
diff --git a/paper/.latexmkrc b/paper/.latexmkrc
index e1b5f1f..6ee0b36 100644
--- a/paper/.latexmkrc
+++ b/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';
 $clean_ext = 'synctex.gz bbl bcf run.xml fls fdb_latexmk glg glo gls ist blg lof lot out toc';
diff --git a/paper/src/chapters/mdp_agent.pdf b/paper/src/chapters/mdp_agent.pdf
index 23cb6e410d59733ee28fbc90b1222f23d31e729e..21460dfb20d52faa2eb8283c3f01db8a7948e373 100644
GIT binary patch
delta 320
zcmV-G0l)sVRkKyFe<**0FcgK~{T1hBOc`jR*4iR{s6rWIAZ_2q9zqOO7)Fvf)_=c5
zt7GKpe%zCD4wr&>G{c5?G3bVRbc<x0c}0QfdLIO$nzcfE0HU|9(fB|Nf-^oRRLZe8
zpx)syDQYE~kqZT%vrb9Skmg|u|7Ogf_fa&_R<YsMaUDw42El*)jS|dsvagsC@T+}H
z;*6w}kUSwYeIfBPA;Dtu7Yk3;+UaYigv;TQP2gQL9XrY&8<*G@=jjeKqq{YBZ>&Hg
zT@@!K#{os*1~<<x6J5~7QpI{bI5&P@@GFcO#WIz4s}kQG7w6N_L7Up~v(R!>TxcY#
z=fw)SnZs*)hkp|VOJ>-YY#;sX4IcIE(l7M<Z$p!jDIWqiIg_#}&J0CBG0mL}3;^Y=
S2|AOEDj*0k3MC~)PeuwX_LOV@

delta 321
zcmV-H0lxmTRkT&Ge<**#FcgK~`zy}Nm@;USSgV!dgDuDy15w|`9zuGlh0&BG9rNEW
zsn#*_bU*INIfu)^BA#K%A_2bS5no}k%A%q`a=!M2<RBZe5rE{att~zvz;MLph)O+l
z4m{d!N5#SDdQfCAQ?fN0Jm%{-#q8o-Z#PLY(#FXC(kdHk)69S8w{Hwd*Xpj4jxeh>
zf{Bc!EEi&ta{j`^Gh_3~<S!PUyminYq@j=_Bpbmy)ves=A0L<bC)Q~Wp7Hz<yK`P(
zkv<fAqlX?v5r#0|Tt+&flcz>@whwOVI^kD1Gte}ZeygJIR?%_43(%(y{76<0Mv=wh
z;d$~x<!<4vzrz&2f~9owOE>p^{s#AYe(4wbe{V>WkSQMmI53m3Db5VVKrzi-3=9C}
TxCuOyiz*-pG72RnMNdWw1C5>E

diff --git a/paper/src/chapters/mdp_human.pdf b/paper/src/chapters/mdp_human.pdf
index 3aa8ceb78da934f89db4f5eff70f5d330f5e6750..e3247c8c7f361640ee1b6dcb1e61a52b10c60122 100644
GIT binary patch
delta 291
zcmV+;0o?wvU9nxTdn|v!YQr!PMDO~Fxs*B-Y)N)(H<%ofKq#dUlHN)WLKcpoSVodd
z^Y@jUIHl;cj~&en%RmV$v8059Eg4}I@~R|FgY5k>C}aoGDMtWguex>k00+eppA*`e
zvG-tPy`B^YYuZsNi$n@-4Oq(Rv_Nw9esHTSn`mdnaMseL#&&;;#q}Gjgx99u39pds
zR-E#Z7L3w5r>uCQ{E^bdZ1NWi55YR>55lULBPN@`n`*V#n4b`rhR2`F8oXRq_t?D;
z0*B(R*jqCWXqq_0`RX#!8Jz;PqIW}dlb0F4z}r#H(>84F)VG%ExZgw=Qb&GN&Wu(n
phy3n&3PS0x;awKE!@q)C;l-EfZvDayZuP>_FZlFtNVAVEA^{pfl&$~(

delta 291
zcmV+;0o?wvU9nxTdn|uZYr-%Th2Qfl&dXS3&?aeZRf-QP$QT1r-^Lz78fsuPB}vEp
z_e-jEj6B_sdvea<GEl-w%qihub4FN&yedguBRgMvh3p_&<p_Z6O*al7;Gj6-b3|J+
zbRLYX*Q4TKO*2Skkw~Gf0ZZ8;Es$Ki@7*fPM%r4@U$k_ovF(3scKgOE;kD^@!Yd@Z
z6{ozU1zmEU7mU47{!Hm?GWm;zr(hlR2Vqsr5tEJJT{T*4%uk3*!{f_x0bb6lN9@iA
zfkW|7?5!Dk)O8%<d~+G;gie84(YZdl$?Jq);q9QNX&bh7>RU^7+;1WbsUtrsX9g>k
pL;mnQ1)=n}@GchI;a|b6@Z!s~_kQ69_j+OJ7yfr|O|y?JA^~Xfkyro#

diff --git a/scripts/nx_paper.sh b/scripts/nx_paper.sh
index 44bce3c..9a864c9 100644
--- a/scripts/nx_paper.sh
+++ b/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
     ;;
   *)