Add documentation comparing Salmon ISR vs auto library type detection

[Copilot]

Documents the behavioral differences between ISR (explicit) and auto (detection) modes for Salmon/alevin library type specification, as requested for understanding the runMultiAlign.sh implementation.

Added Documentation

• salmon_library_types.md - Comprehensive reference covering:
  • ISR mode: explicit orientation (faster, requires known protocol)
  • Auto mode: runtime detection (~5M read sampling, handles uncertainty)
  • Trade-offs: speed vs robustness comparison table
  • Current repo usage: --expected-ori fw for 10x Chromium
  • Migration guide: tool-specific syntax for simpleaf/salmon/piscem

Key Differences

Mode	Speed	Use When
ISR/fw	Faster (no detection)	Standard 10x, validated protocols
Auto	+detection overhead	Unknown protocols, troubleshooting

Example Migration

# Current (explicit)
--expected-ori fw --unfiltered-pl

# Auto mode (simpleaf)
--expected-ori both --unfiltered-pl

Includes verification steps and version-specific caveats for safe adoption.

Original prompt

Can you look at the salmon repo for me and tell me what the difference in behavior is between ISR and auto mode

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