Fix issues with v2 config parser

[robsyme]

Problem

On the 25.10.x line, the strict (v2) config parser aborts a run at config-build time with Unknown configuration profile: '<name>' whenever the profiles {} block lives in a config file that is not the last one parsed. The legacy (v1) parser handles the same configuration fine.

This surfaces on Seqera Platform launches in particular: Platform writes a config into the launch directory (a tower {} scope, no profiles) which is parsed after the pipeline's own nextflow.config, so every profile-using pipeline fails under the v2 parser. It reproduces with plain nextflow config/nextflow run against two config files; includeConfig is not involved.

Root cause

ConfigBuilder creates a single ConfigParser instance and calls parse() for each config file in order, then validates the requested -profile againstparser.getDeclaredProfiles() once at the end.

ConfigParserV2 reassigned its declaredProfiles field on every parse()call (declaredProfiles = script.getDeclaredProfiles()), so the field ended up holding only the profiles from the last file parsed. The v1 parser keeps a final set and adds to it, accumulating across all files.

Fix

Initialise declaredProfiles to an empty set and accumulate with addAll(...) across parse() calls, matching the v1 behaviour. Two lines.

This is already fixed on the default branch as part of the larger #6643 ("enable v2 syntax parser by default"), which can't be cherry-picked cleanly onto 25.10.x; this PR is the minimal extraction of just the profile-accumulation fix.

Verification

• New regression test should accumulate declared profiles across multiple config files reuses one parser across two parse() calls (the second declaring no profiles) and asserts the earlier file's profiles are retained.
• Confirmed the test fails on the unpatched 25.10.x branch and passes with the fix; the rest of ConfigParserV2Test is unchanged and green.

Scope / risk

The only non-test consumer of getDeclaredProfiles() is ConfigBuilder's checkValidProfile gate, so the blast radius is limited to profile validation. The v2 parser is opt-in on 25.10.x (NXF_SYNTAX_PARSER=v2).

[bentsherman]

@robsyme does this also fix #6623 ? or is that a different bug? it was also fixed by #6643 but was never backported to 25.10

that bug is also a likely blocker so we might as well make sure it is fixed as well

[robsyme]

Heya Ben.

No, this PR does not fix #6623. They're separate bugs with separate fixes.

Both bugs were fixed together in #6643, but by two independent code changes - my PR here only picks out one of those fixes.

The two fixes are:

Profile accumulation (the one this PR backports) - my customer bug
ConfigParserV2: declaredProfiles = script.getDeclaredProfiles() → declaredProfiles.addAll(...). Fixes the loud Unknown configuration profile failure.

Params from includeConfig (issue #6623)
In 25.10.x, ConfigDsl.setParams() aliases target.params = paramOverrides, and assign() skips any param already in paramOverrides. When an active profile does includeConfig, the include is parsed with .setParams(target.params) - so the main config's declared params get passed in as if they were CLI overrides, and the included file's assignment is silently skipped. #6643 fixed this by splitting cliParams (true --param overrides, which should win) from configParams (accumulated config values, for reference only). This PR currently does not touch this path.

How about I adjust this PR to backport both fixes?