Apply the configuration bundled in a pipeline file as the lowest argument layer

[johnchase]

What

A .adg now carries its values in a configs list (see adagio-app feat/adg-configs), in the arguments-file shape. The CLI applies the first bundled config as the lowest layer:

1. config bundled in the .adg
2. --arguments file
3. command-line flags

• adagio run reads it under --arguments and flags; --help and --show-params resolve defaults and "missing" through the same layers.
• --no-bundled-config ignores it (Nextflow's -C for this file).
• adagio pipeline config <pipeline> prints the bundled config as an arguments file to save, edit and pass back.
• adagio runtime --spec (adapter path) applies it under the job's arguments when the spec file is a full envelope.
• Signatures no longer carry defaults (required defaults to true); files written before configs existed still supply signature.parameters[].default and meta.editor_variables[].value as a bundled config.
• A bundled value for a variable nothing uses yet is skipped, not refused; unknown names in a user's own --arguments file are still errors.

Tests

271 passed; new tests/test_bundled_config.py covers precedence, the flag, legacy lift, unused-variable tolerance, the config command and the runtime path.