Add WorkflowInterceptor extension point for named-workflow plugins

[huangzhibo]

Context

Relates to #5589 (checkpoint / skip-forward discussion).

Adds a minimal pf4j ExtensionPoint — nextflow.plugin.WorkflowInterceptor — that lets a plugin wrap the execution of named workflows. The core change is tiny; the actual stage-archiving / reuse logic lives in a separate plugin, nf-stage, which is the first consumer.

What changes

• New interface WorkflowInterceptor in nf-commons (32 lines)
• WorkflowDef.run() looks up an interceptor via Plugins.getExtension(WorkflowInterceptor); if one is registered, delegates to it with a proceed closure that runs the original body (13 lines, extracted into runDefault())
• Entry workflows (name == null) are never intercepted
• Behavior is unchanged when no plugin is installed

Total: +45 / -0 across 2 files.

API

interface WorkflowInterceptor extends ExtensionPoint {
    Object intercept(Object workflow, Object[] args, Closure proceed)
}

The interceptor owns the invocation: it may mutate args (e.g. clone channel inputs in place) before calling proceed(), and post-process the returned ChannelOut. Whether and when proceed() is invoked, and how the result channels are driven, is the plugin's responsibility.

Why an extension point

Issue #5589 surfaces two positions: users want stage-level skip-forward semantics; core maintainers want -resume left alone and prefer pipeline authors prototype the pattern first. An extension point sidesteps the tension — it doesn't add any user-facing semantics to core, but unblocks plugin-side experimentation. If a pattern proves out in a plugin, promoting it to core remains an option later.

Consumer: nf-stage

nf-stage uses this hook to archive each named workflow's emit: outputs on first run and, on reruns, replay them from a content-addressed archive when a SHA-256 digest over (stage name, static args, channel input contents) matches — no work/ dependency, no per-task hash. The mechanics (clone channel args into args[], let proceed() wire processes onto the clones, decide after digest compute whether to feed clones or STOP them) rely on the interceptor controlling args mutation and post-proceed channel flow, which is why the hook signature includes args[] and a proceed closure rather than simple before/after callbacks.

Test plan

• Existing WorkflowDef tests pass (no behavior change without a plugin)
• Validated in nf-stage end-to-end: named sub-workflows intercepted, entry workflow not intercepted, proceed() round-trips ChannelOut correctly
• Happy to add a core-side test with a mock interceptor if reviewers prefer

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