From f027ac173603ecb55e0631bf671f46ed8a7cc079 Mon Sep 17 00:00:00 2001
From: Daniel Rosel <daniel@alves.world>
Date: Thu, 9 Apr 2026 23:07:56 +0200
Subject: [PATCH] updating with TOC

---
 paper/src/chapters/mdp_agent.pdf | Bin 10932 -> 10932 bytes
 paper/src/chapters/mdp_human.pdf | Bin 11953 -> 11953 bytes
 paper/src/main.tex               |   2 ++
 scripts/nx_paper.sh              |  20 +++++++++++++++++---
 4 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/paper/src/chapters/mdp_agent.pdf b/paper/src/chapters/mdp_agent.pdf
index d06b268a806d678feb84f41fa9862c84fc58acec..23cb6e410d59733ee28fbc90b1222f23d31e729e 100644
GIT binary patch
delta 291
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diff --git a/paper/src/chapters/mdp_human.pdf b/paper/src/chapters/mdp_human.pdf
index a04e427b9c7587013a73e7e01ba883f6022417ba..3aa8ceb78da934f89db4f5eff70f5d330f5e6750 100644
GIT binary patch
delta 284
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diff --git a/paper/src/main.tex b/paper/src/main.tex
index a5ce990..2959d04 100644
--- a/paper/src/main.tex
+++ b/paper/src/main.tex
@@ -33,6 +33,8 @@ Factorial training on TPUs shows the expected short-run revenue hit from contami
 \vspace{0.5em}
 \noindent\textbf{Project page:} \url{https://velocitatem.github.io/PHANTOM/}
 
+\clearpage
+\tableofcontents
 \clearpage
 \input{chapters/01-intro}
 \input{chapters/02-literature-review}
diff --git a/scripts/nx_paper.sh b/scripts/nx_paper.sh
index f4a28d8..44bce3c 100644
--- a/scripts/nx_paper.sh
+++ b/scripts/nx_paper.sh
@@ -27,6 +27,20 @@ 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"
+  }
+}
+
 case "$cmd" in
   build)
     mkdir -p paper/build
@@ -34,7 +48,7 @@ case "$cmd" in
     bash paper/concat_code.sh
     cd paper/src
     link_build_bib
-    latexmk -pdf -jobname=main -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build main.tex
+    latexmk_paper main main.tex
     ;;
   watch)
     mkdir -p paper/build
@@ -63,7 +77,7 @@ case "$cmd" in
     sync_mdp_figures
     cd paper/src
     link_build_bib
-    latexmk -pdf -jobname=main-genpop -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build main-genpop.tex
+    latexmk_paper main-genpop main-genpop.tex
     ;;
   watch-genpop)
     mkdir -p paper/build
@@ -85,7 +99,7 @@ case "$cmd" in
     mkdir -p paper/build
     cd paper/src
     link_build_bib
-    latexmk -pdf -jobname=summary -f -interaction=nonstopmode -file-line-error -r ../.latexmkrc -outdir=../build summary.tex
+    latexmk_paper summary summary.tex
     ;;
   watch-summary)
     mkdir -p paper/build