Adds a `_strip_think` function using `awk` to buffer stdin and track the last `</think>` tag, emitting only the subsequent content. This utility is now piped after `aichat` calls to remove AI reasoning blocks before commit message generation. Also applies minor whitespace and indentation adjustments throughout the script.
Refactors `startIter` to separate the traversal into two distinct passes: one for chain starts (nodes without left extension) and another specifically targeting cycle nodes. Also simplifies `nextUnitigKmer` by removing the redundant `_at_start_ parameter and unifying traversal direction logic. Updates `UnitigIter` to manage visited marking internally, improving encapsulation and cycle detection reliability.
Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
Eric Coissac