docs: remove in-tree design docs and gitignore docs/design/

[nh13]

Deletes the two design docs under docs/design/ and adds docs/design/ to .gitignore so design/spec documents are no longer tracked in the repository.

Removed:

• docs/design/deterministic-mi-numbering.md
• docs/design/sort-phase2-unification-deferral.md

The .gitignore entry keeps future design/spec docs out of the tree.

Risk: command output changes — none; unsafe changes — none, and CLAUDE.md allowlist changes — none; memory, queue, thread, or backpressure policy changes — none. Fix: remove obsolete design documents and ignore future files under docs/design/.

• Deleted two design documents.
• Added docs/design/ to .gitignore.

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• .gitignore
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• docs/design/deterministic-mi-numbering.md
• docs/design/sort-phase2-unification-deferral.md
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• src/lib/pipeline/steps/group/position.rs
• src/lib/unified_pipeline/bam.rs

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Walkthrough

The change removes obsolete design documents, ignores docs/design/, and updates source comments and migration guidance to remove stale references. MI numbering documentation now describes serial assignment behavior.

Changes

Design documentation cleanup

Layer / File(s)	Summary
Design document removal .gitignore, docs/design/deterministic-mi-numbering.md, docs/design/sort-phase2-unification-deferral.md	.gitignore now excludes docs/design/. Both design documents are deleted.
Reference and behavior documentation cleanup crates/fgumi-sort/src/merge_slots.rs, crates/fgumi-sort/src/worker_pool.rs, docs/src/guide/migration-from-fgbio.md, src/lib/commands/dedup.rs, src/lib/pipeline/steps/group/position.rs, src/lib/unified_pipeline/bam.rs	Stale design-document references are removed. Comments now describe the current serial MI assignment and ordinal behavior.

Priority: ⬇️ Low

Estimated code review effort: 1 (Trivial) | ~2 minutes

Change: Other

Merge Risk: 🔵 Low · up to 06ca7

This change removes obsolete design documents and cleans related references, but an open concern remains that deleted-document references may still be present. This could leave users or maintainers following stale documentation, so the change is mergeable with owner awareness.

Suggested labels: fgumi sort

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title uses the required Conventional Commit format and accurately describes removing the design documents and adding docs/design/ to .gitignore.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.34%. Comparing base (6a290a8) to head (2699432).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #934      +/-   ##
==========================================
- Coverage   94.36%   94.34%   -0.02%     
==========================================
  Files         303      303              
  Lines      150442   150442              
==========================================
- Hits       141963   141938      -25     
- Misses       8479     8504      +25     

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Actionable comments posted: 1

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Inline comments:
In @.gitignore:
- Line 45: Remove or replace all references to deleted files under docs/design/
in merge_slots.rs, migration-from-fgbio.md, and position.rs. Point references to
the appropriate replacement documentation where available; otherwise remove
them, while preserving the surrounding content and behavior.

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