From b6c1c26a5d411ba92e128d838af7d10fbcf6133c Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Wed, 24 Jun 2026 20:01:25 +0200
Subject: [PATCH] (v3.0.1.9068) todo tracker update

---
 .github/workflows/todo-tracker.yml | 20 +++++++++++++-------
 DESCRIPTION                        |  2 +-
 NEWS.md                            |  2 +-
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/todo-tracker.yml b/.github/workflows/todo-tracker.yml
index 0c506badc..921539737 100644
--- a/.github/workflows/todo-tracker.yml
+++ b/.github/workflows/todo-tracker.yml
@@ -87,14 +87,15 @@ jobs:
           > /tmp/issues_seen.txt
 
           while IFS= read -r match; do
-            file=$(echo "$match" | sed 's|^\./||' | cut -d: -f1)
-            lineno=$(echo "$match" | sed 's|^\./||' | cut -d: -f2)
-            text=$(echo "$match" | sed 's|^\./||' | cut -d: -f3-)
+            clean=$(printf '%s\n' "$match" | sed 's|^\./||')
+            file=$(printf '%s\n' "$clean" | cut -d: -f1)
+            lineno=$(printf '%s\n' "$clean" | cut -d: -f2)
+            text=$(printf '%s\n' "$clean" | cut -d: -f3-)
 
             # determine marker type (first match wins, TODO is default)
             marker="TODO"
             for m in FIXME HACK XXX; do
-              if echo "$text" | grep -qw "$m"; then marker="$m"; break; fi
+              if printf '%s\n' "$text" | grep -qw "$m"; then marker="$m"; break; fi
             done
 
             # git blame timestamp
@@ -109,7 +110,7 @@ jobs:
             fi
 
             # extract issue references (#NNN)
-            issues=$(echo "$text" | grep -oE '#[0-9]+' | sed 's/#//' | tr '\n' ',' | sed 's/,$//' || true)
+            issues=$(printf '%s\n' "$text" | grep -oE '#[0-9]+' | sed 's/#//' | tr '\n' ',' | sed 's/,$//' || true)
             if [ -n "$issues" ]; then
               for inum in $(echo "$issues" | tr ',' ' '); do
                 echo "$inum" >> /tmp/issues_seen.txt
@@ -197,7 +198,10 @@ jobs:
                   age_str=$(format_age "$d")
                   flag=""
                   [ "$d" -gt "$STALE_DAYS" ] 2>/dev/null && flag=" :warning:"
-                  echo "- \`${f}\` L${l} (${age_str} ago)${flag}"
+                  # re-read the actual source line and trim leading/trailing whitespace
+                  src_text=$(sed -n "${l}p" "$f" 2>/dev/null | sed 's/^[[:space:]]*//;s/[[:space:]]*$//' || true)
+                  echo "- [\`${f}\` L${l}](${REPO_URL}/${f}#L${l}) (${age_str} ago)${flag}"
+                  [ -n "$src_text" ] && echo "  \`${src_text}\`"
                 done
 
                 echo ""
@@ -242,7 +246,9 @@ jobs:
               flag=""
               [ "$age_days" -gt "$STALE_DAYS" ] 2>/dev/null && flag=" !!"
 
-              printf 'L%s: %s  ◁ %s ago%s\n' "$lineno" "$text" "$age_str" "$flag"
+              # re-read the actual source line to avoid TSV round-trip corruption
+              src_line=$(sed -n "${lineno}p" "$file" 2>/dev/null | sed 's/[[:space:]]*$//' || true)
+              printf 'L%s: %s  ◁ %s ago%s\n' "$lineno" "$src_line" "$age_str" "$flag"
 
               prev_file="$file"
               prev_lineno="$lineno"
diff --git a/DESCRIPTION b/DESCRIPTION
index 31759a334..57a4e44aa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9067
+Version: 3.0.1.9068
 Date: 2026-06-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 3af85e9d4..e789f2c3d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9067
+# AMR 3.0.1.9068
 
 Planned as v3.1.0, end of June 2026.