Preserve hand-written entries when regenerating container configs

[pinin4fjords]

Summary

• generate_container_configs() (behind nf-core pipelines lint --fix container_configs and bulk modules update/remove/patch) unconditionally deleted and rewrote every conf/containers_*.config file from a fresh meta.yml scan, with no way to keep hand-written entries for modules that don't carry per-platform containers: metadata yet.
• This is the marker convention the Seqera Containers Part 2 blog post describes (// AUTOGENERATED CONFIG BELOW THIS POINT - DO NOT EDIT), but it was never actually implemented when the generation feature shipped in Command to generate pipeline container config files #3955 - I found this while trying to adopt the scheme in nf-core/rnaseq and hit real data loss risk from it.
• Content above the marker is now preserved verbatim on every regeneration path (generate_container_configs() full scan and update_module_container_config() single-module update); only the generated section below the marker is replaced. Files with no generated entries but existing manual content are kept rather than deleted. Files without a marker at all (i.e. anything written by a pre-this-PR version of the tool) are treated as fully generated, matching current behaviour, so nothing changes for existing pipelines until they add manual content above a marker themselves.
• Updated the container_configs lint docstring to document the convention.

Test plan

• Added tests covering: manual prefix survives a full regen, a removed module's generated entry disappears while manual content stays, a manual-only file (no generated entries) isn't deleted, and the single-module update path also preserves manual content.
• uv run pytest tests/pipelines/test_container_configs.py tests/pipelines/lint/test_container_configs.py - 14 passed
• uv run ruff check / uv run ruff format --check on changed files - clean
• uv run mypy on changed files - no new errors (pre-existing errors elsewhere in the codebase are unrelated to this change)
• Confirmed against a clean dev checkout that the unrelated tests/modules/ failures in this sandbox (network access to GitHub/GitLab) are pre-existing and not caused by this change

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 95.45455% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.22%. Comparing base (d91668e) to head (1fe2807).

Files with missing lines	Patch %	Lines
nf_core/pipelines/containers_utils.py	95.45%	1 Missing ⚠️

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