fix(run): preserve job dependencies when tasks are skipped

[mmorvan]

Closes #39

Description

When tasks were skipped via --skip or [stages] skip, the job dependency chain between cycles was silently broken. Tasks in cycle N+1 lost their dependency on cycle N's jobs whenever cycle N was entirely skipped, allowing cycles to run out of order on the scheduler.

The same issue affected sequential task groups: if task A in [A -> B] was skipped, task B lost the dependency on the previous sequence's jobs.

Root cause — three assignments in Workflow.run() unconditionally overwrote dependency lists with an empty list when no jobs were submitted:

task_depend = task_jobs          # [] when task was skipped
sequence_depend = sequence_jobs  # [] when whole cycle was skipped
stage_jobs = sequence_jobs       # [] propagated to epilog

Fix — only update each variable when jobs were actually submitted; fall back to the preserved value otherwise:

if task_jobs:
    task_depend = task_jobs
if sequence_jobs:
    sequence_depend = sequence_jobs
stage_jobs = sequence_depend     # use the preserved value

Check list

• Closes Bug: inter-cycle dependencies lost when --skip is use #39
• Tests added
• User visible changes (including notable bug fixes) are documented in CHANGES.rst
• New modules are listed in api.rst