Route progress, banners and log fallbacks to stderr

Some Nextflow commands now emit machine-readable output on stdout (nextflow inspect -o json, nextflow run outputs, etc.). Today, log messages, progress UI, banners and spinners are also written to stdout, which makes that output difficult to pipe into downstream tools (jq, etc.).

This change applies a simple rule: a command's main output stays on stdout; everything else (progress, status, banners, log fallbacks) moves to stderr. Human-readable command output (e.g. --help, --version, nextflow info, nextflow view, nextflow list) is unaffected — it remains on stdout because it is the main output of those commands.

Files changed

• modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy — the global logback appender's System.out fallback (used when no AnsiLogObserver is registered, or the observer isn't started yet) now writes to System.err. Highest leverage change: affects log output from every command, including the "Monitor the execution with Seqera Platform" sticky message that breaks nextflow inspect | jq today.
• modules/nextflow/src/main/groovy/nextflow/trace/AnsiLogObserver.groovy — progress rendering, summary block, and info/warning/error UI panels now use AnsiConsole.err instead of AnsiConsole.out. AnsiConsole.systemInstall() is unchanged.
• modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy — the N E X T F L O W ~ version … banner and the Launching … [run-name] - revision: … line now use AnsiConsole.err.
• modules/nextflow/src/main/groovy/nextflow/util/SpinnerUtil.groovy — animated spinners (and the non-ANSI plaintext fallback in stopWithMessage) now write to stderr.
• modules/nextflow/src/main/groovy/nextflow/trace/AgentLogObserver.groovy — class-level docstring corrected to say "standard output" instead of "standard error". The implementation, the integration tests, and the design intent all agree that the structured [PIPELINE]/[WORKDIR]/[SUCCESS] lines emitted in NXF_AGENT_MODE are the meaningful programmatic output of agent mode and belong on stdout; only the docstring was wrong.

Deliberately unchanged

• Session.printConsole() stays on stdout. It is the data path used by the view() channel operator, echo true task stdout forwarding, and the workflow output {} DSL block — i.e. exactly the kind of programmatic output stdout is for.
• AgentLogObserver output streams — agent-mode structured output ([PIPELINE], [WORKDIR], [SUCCESS], [ERROR], [FAILED], etc.) stays on stdout. In NXF_AGENT_MODE these lines are the main output, designed to be parsed by AI tooling.
• --help, --version, nextflow info, nextflow view, nextflow list, nextflow clean, nextflow clone, nextflow plugin create, nextflow log, nextflow lineage, nextflow inspect, nextflow config, nextflow lint, nextflow fs, nextflow secrets, wave, etc. — these all already write their main output on stdout and are unaffected.
• nf-tower LaunchCommandImpl — nextflow launch currently mixes its banner and the workflow ID on stdout. Left for a follow-up that can introduce a JSON output mode.
• nf-tower AuthCommandImpl — interactive prompts and confirmations stay on stdout (these commands aren't piped).

Net effect

nextflow inspect | jq, nextflow run … | … (and equivalents for other pipeable commands) no longer have stdout polluted by progress UI, banners, spinners, or log fallbacks. The "Monitor the execution with Seqera Platform using this URL: …" sticky message in particular — which is emitted via log.info(STICKY, …) from the Tower observer — now correctly lands on stderr in commands like nextflow inspect because it falls through the no-observer path in LoggerHelper.

Verification

• ./gradlew :nextflow:compileGroovy passes.
• agent-output.nf and agent-output-error.nf integration tests pass: [PIPELINE]/[WORKDIR]/[SUCCESS] lines from AgentLogObserver and World received: Hello from agent mode from Session.printConsole() continue to land on stdout, as the tests assert.