Fix workflow being skipped and marked as failed when agent starts before server

[6543]

reported at #6355 (comment)

When the agent started before the server was available, it retried the connection as expected. However, once the server came up and a workflow was picked up, the pipeline would immediately fail without running any steps — the agent logs showed workflow context done firing instantly after received execution.

The root cause was a package-level shutdownCtx shared across retry iterations. On each failed attempt, stopAgentFunc stamped it with a 5-second timeout — starting the clock immediately. By the time the agent successfully connected and received a workflow, workflowCtx was derived from this already-expired context, so execution failed before Docker even started a container.

The fix removes the global mutable shutdown context and the stopAgentFunc indirection. Instead, runner.Run() no longer accepts a shutdownCtx parameter — it creates a fresh one locally only when needed for the Done() fallback call. The healthcheck server shutdown does the same. This makes the lifetime of each shutdown window explicit and local.

[codecov]

Codecov Report

❌ Patch coverage is 0% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 34.19%. Comparing base (2de5962) to head (41e267a).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
agent/runner.go	0.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #6361      +/-   ##
==========================================
- Coverage   34.20%   34.19%   -0.01%     
==========================================
  Files         426      426              
  Lines       28537    28541       +4     
==========================================
  Hits         9760     9760              
- Misses      17889    17893       +4     
  Partials      888      888              

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[6543]

one of the bugs was actually a regression of #6021 ... b.t.w. ... but with this refactoring we did more fixing and preventing :)