nextflow lint: support reading file paths from a file or stdin to avoid ARG_MAX limits #6857

Feature Request

Problem

When integrating nextflow lint with tools like pre-commit, all matching filenames are passed as CLI arguments. On large repositories (e.g. nf-core/modules with 1700+ .nf files), this exceeds the OS ARG_MAX limit (~2MB on Linux, shared between argv + envp), causing E2BIG errors:

nextflow: line 287: /usr/bin/dirname: Argument list too long
nextflow: line 323: /usr/bin/sed: Argument list too long
nextflow: line 327: java: Argument list too long

The current workaround is to batch files into multiple nextflow lint invocations (see seqeralabs/nf-lint-pre-commit#4), but this means multiple JVM startups and requires capturing output to present a clean summary.

Proposed Solution

Support reading file paths from a file or stdin, e.g.:

# Option A: response file (like javac @argfile)
nextflow lint @filelist.txt

# Option B: --files-from flag
nextflow lint --files-from filelist.txt

# Option C: stdin
find . -name '*.nf' | nextflow lint --stdin

Any of these would allow a single nextflow lint invocation regardless of file count, avoiding the ARG_MAX limit entirely.

Context

• Reported in CI: https://github.com/nf-core/modules/actions/runs/22347821806/job/64668726513?pr=10241#step:4:156
• Related (CI-friendly logging): nextflow lint ignores --quiet flag #6856
• Current workaround: fix: batch files in lint hook to avoid ARG_MAX on large repos seqeralabs/nf-lint-pre-commit#4