fix: ensure jiraticket survives eval parse_yaml in update_config.sh

Root cause: eval $(parse_yaml config.yml) inside update_config.sh was
silently overwriting $jiraticket (set by the lookup) because the YAML
key and pipeline variable share the same name. 00_unpack_zip.sh and
other downstream scripts also call eval parse_yaml, compounding the
problem.

Fix:
- update_config.sh: save $jiraticket before eval, restore it after so
  pipeline/environment value takes precedence over config.yml value
- Both populate pipelines: move ./tools/update_config.sh to immediately
  after the jiraticket lookup (before 00_unpack_zip.sh and friends),
  so jiraticket is committed to config.yml before any script can clobber it

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: larsvilhuber

bitbucket-pipelines.yml

@@ -245,6 +245,7 @@ pipelines:
             - projectID="${projectID:-zenodo-$ZenodoID}"
             - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
             - if [ -z "$jiraticket" ] && [ -n "${openICPSRID:-}" ]; then jiraticket=$(python3 tools/jira_find_task_by_icpsr.py "$openICPSRID" 2>/dev/null || true); fi
+            - ./tools/update_config.sh
             - if [ -d cache ]; then ls -lR cache/*; fi
             - ls -l generated/*
             # repeat this part
@@ -257,7 +258,6 @@ pipelines:
             - ./automations/21_cleanup.sh     $projectID
             - ./automations/25_replace_report.sh
             - ./automations/30_cleanup_aux.sh
-            - ./tools/update_config.sh
             - ./automations/20_commit_code.sh config.yml notag
             - git status
             - git push && git push --tags
@@ -422,6 +422,7 @@ pipelines:
             - projectID="${openICPSRID}"
             - projectID="${projectID:-zenodo-$ZenodoID}"
             - if [ -z "$jiraticket" ] && [ -n "${openICPSRID:-}" ]; then jiraticket=$(python3 tools/jira_find_task_by_icpsr.py "$openICPSRID" 2>/dev/null || true); fi
+            - ./tools/update_config.sh
             - if [ -d $projectID ]; then \rm -rf $projectID; fi
             - if [ ! -z $openICPSRID ]; then python3 tools/download_openicpsr-private.py $openICPSRID; fi
             - if [ ! -z $ZenodoID ]; then python3 tools/download_zenodo_draft.py $ZenodoID; fi
@@ -442,7 +443,6 @@ pipelines:
             - ./automations/21_cleanup.sh     $projectID
             - ./automations/25_replace_report.sh
             - ./automations/30_cleanup_aux.sh
-            - ./tools/update_config.sh
             - ./automations/20_commit_code.sh config.yml notag
             - git status
             - git push

tools/update_config.sh

@@ -17,6 +17,11 @@ if [ ! -f config.yml ]; then
     fi
 fi
 
+# Save pipeline-provided values before eval overwrites them.
+# config.yml and pipeline vars share the same key name for jiraticket, so
+# eval $(parse_yaml ...) silently clobbers the pipeline/environment variable.
+_env_jiraticket="${jiraticket:-}"
+
 # read parameters
 eval $(parse_yaml config.yml)
 
@@ -36,7 +41,8 @@ ZenodoID="${ZenodoID:-$zenodo}"
 DataverseID="${DataverseID:-$dataverse}"
 OSFID="${OSFID:-$osf}"
 MainFile="${MainFile:-$main}"
-jiraticket="${jiraticket:-$jiraticket}"
+# Restore pipeline/environment value if it was set; otherwise keep config.yml value
+jiraticket="${_env_jiraticket:-$jiraticket}"
 mcid="${mcid:-$mcid}"
 
 # write it back