Adopt shared ccbr_tools pipeline logging library in aspen wrapper (Phase B)

[kopardev]

Summary

Follow-up to #119 (Phase A: port CARLISLE's progress monitor +
enriched pipeline.status.json fields into aspen). Once that lands and the
ported implementation is stable, replace ASPEN's locally-duplicated logging/
state-marker bash functions with a shared library sourced from ccbr_tools,
so ASPEN and CARLISLE stop maintaining two independent copies of the same
code.

Tracked centrally in CCBR/Tools#230 (adds scripts/ccbr_pipeline_logging.sh
to ccbr_tools, installed onto PATH via module load ccbrpipeliner).

Proposed work (ASPEN side)

1. Once Add shared pipeline logging/state-marker bash library for ASPEN/CARLISLE Tools#230 publishes ccbr_pipeline_logging.sh, replace the
   inline definitions of log_info/log_step/log_ok/log_warn/log_error/
   log_next/log_divider, json_escape, print_versions,
   write_pipeline_state_marker, run_jobby_best_effort, and
   _progress_monitor in aspen with a sourcing shim:

   command -v ccbr_pipeline_logging.sh >/dev/null 2>&1 || module load ccbrpipeliner >/dev/null 2>&1 || true
   source "$(command -v ccbr_pipeline_logging.sh)"
   

   mirroring the existing run_jobby_best_effort module-load-if-missing
   fallback pattern already used in aspen.
2. Set ASPEN-specific env vars (PIPELINE_NAME=ASPEN, snakemake log path
   ${WORKDIR}/snakemake.log — note ASPEN keeps this at the workdir root, NOT
   under a logs/ subfolder like CARLISLE) before sourcing.
3. Add a syncscripts/rescript runmode to aspen's main() case statement
   using the new shared helper from Add shared pipeline logging/state-marker bash library for ASPEN/CARLISLE Tools#230, to re-sync
   workflow/scripts into an existing workdir without a full reset.
4. Prerequisite: extend ASPEN's check_essential_files() to also verify
   ESSENTIAL_FOLDERS (currently only checks config.yaml/samples.tsv/
   cluster.json/tools.yaml, unlike CARLISLE's version which checks both
   ESSENTIAL_FILES and ESSENTIAL_FOLDERS) — needed so syncscripts can
   safely assume the scripts/ folder exists in WORKDIR.
5. Verify end-to-end on ASPEN's .test/ dataset: no behavioral/log-format
   regressions vs. the pre-refactor wrapper.

Related

• Depends on: feat(aspen): port CARLISLE structured logging, state markers, and jobby integration #119 (Phase A, must land first)
• Depends on: Add shared pipeline logging/state-marker bash library for ASPEN/CARLISLE Tools#230 (shared library must be published first)
• Companion issue: CCBR/CARLISLE (adopt the same library in carlisle)

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