fix: strip AI reasoning blocks from commit messages

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.

scripts/jj_commit_msg.sh

@@ -22,6 +22,21 @@ log()  { printf '\033[1;34m==>\033[0m %s\n' "$*" >&2; }
 info() { printf '      \033[0;37m%s\033[0m\n' "$*" >&2; }
 ok()     { printf '      \033[0;32m✓\033[0m %s\n' "$*" >&2; }
 
+# _strip_think — remove reasoning tags from stdin
+# Buffer all input, locate the LAST </think> line, emit only what follows.
+# This handles think blocks that themselves contain </think> fragments.
+_strip_think() {
+    awk '{
+        lines[NR] = $0
+        print $0 > "/dev/stderr"
+        if (/^<\/think>/) last_end = NR
+    }
+    END {
+        start = (last_end ? last_end + 1 : 1)
+        for (i = start; i <= NR; i++) print lines[i]
+    }'
+}
+
 # _readable_diff <file>
 #   Returns a human-readable diff for <file>.
 #   For pathological single-line formats (JSON, minified JS/CSS…), pretty-prints
@@ -104,7 +119,7 @@ while IFS= read -r file; do
     n=$((n + 1))
     log "[$n/$file_count] Summarising $file …"
 
-    summary=$(printf '%s' "$diff" | aichat "In 2-3 lines, summarise what this diff changes in the file '$file'. Be concise and technical.")
+    summary=$(printf '%s' "$diff" | aichat "In 2-3 lines, summarise what this diff changes in the file '$file'. Be concise and technical." | _strip_think)
 
       # Print the summary indented to stderr
     while IFS= read -r line; do
@@ -123,10 +138,10 @@ if [[ -z "$summaries" ]]; then
 fi
 
 log "Generating commit message from $n summary/summaries …"
-result=$(printf '%s' "$summaries" | aichat "From these per-file summaries of a jj diff, write a single conventional commit message in English. First line: short imperative summary (max 72 chars). Then a blank line. Then a short paragraph with more detail if needed. Output only the commit message, nothing else.")
+result=$(printf '%s' "$summaries" | aichat "From these per-file summaries of a jj diff, write a single conventional commit message in English. First line: short imperative summary (max 72 chars). Then a blank line. Then a short paragraph with more detail if needed. Output only the commit message, nothing else." | _strip_think)
 
 ok "Done"
 printf '\n' >&2
 
-# Commit message goes to stdout
-printf '%s\n' "$result"
+# Commit message goes to stdout (strip leading blank lines so jj sees content)
+printf '%s\n' "$result" | sed '/./,$!d'

src/obikseq/src/lib.rs

@@ -12,6 +12,7 @@ pub mod kmer;
 mod revcomp_lookup;
 /// Routable super-kmer: canonical sequence paired with its minimizer for scatter routing.
 pub mod routable;
+mod sequence;
 pub mod superkmer;
 
 pub mod unitig;
@@ -19,4 +20,5 @@ pub mod unitig;
 pub use annotations::Annotation;
 pub use kmer::CanonicalKmer;
 pub use routable::RoutableSuperKmer;
+pub use sequence::Sequence;
 pub use superkmer::SuperKmer;

src/obikseq/src/sequence.rs

@@ -1,5 +1,8 @@
+use crate::Annotation;
+
 pub trait Sequence {
-    fn sequence(&self) -> &[u8];
-    fn canonical(&self) -> Self;
+    fn sequence(&self) -> Box<[u8]>;
+    fn canonical(&self) -> &Self;
     fn seq_hash(&self) -> u64;
+    fn annotation(&self) -> Annotation;
 }

src/obikseq/src/superkmer.rs

@@ -1,13 +1,14 @@
 //! Compact 2-bit DNA super-kmer with in-place reverse complement and canonical form.
 use std::io::{self, Write};
 
+use bitvec::prelude::*;
 use serde::Serialize;
+use xxhash_rust::xxh3::xxh3_64;
 
+use crate::Sequence;
 use crate::encoding::{DEC4, encode_base};
 use crate::kmer::{CanonicalKmer, Kmer, KmerError};
 use crate::revcomp_lookup::REVCOMP4;
-use bitvec::prelude::*;
-use xxhash_rust::xxh3::xxh3_64;
 
 // ── SuperKmerHeader ───────────────────────────────────────────────────────────
 
@@ -53,7 +54,7 @@ impl SuperKmerHeader {
 }
 
 #[derive(Serialize)]
-struct CountAnnotation {
+struct SKAnnotation {
     seq_length: usize,
     kmer_size: usize,
     minimizer_size: usize,
@@ -90,6 +91,22 @@ impl std::hash::Hash for SuperKmer {
     }
 }
 
+impl Sequence for SuperKmer {
+    fn sequence(&self) -> Box<[u8]> {
+        self.seq.clone()
+    }
+
+    fn canonical(&self) -> &Self {
+        &self
+    }
+
+    /// Returns the XXH3-64 hash of the packed sequence bytes.
+    fn seq_hash(&self) -> u64 {
+        xxh3_64(&self.seq)
+    }
+
+    fn annotation(&self) -> Annotation {}
+}
 impl SuperKmer {
     /// `seql` is the raw stored byte: 1–255 for lengths 1–255, 0 for length 256.
     pub fn new(seql: u8, seq: Box<[u8]>) -> Self {
@@ -315,11 +332,6 @@ impl SuperKmer {
     pub fn iter_canonical_kmers(&self, k: usize) -> impl Iterator<Item = CanonicalKmer> + '_ {
         self.iter_kmers(k).map(move |km| km.canonical(k))
     }
-
-    /// Returns the XXH3-64 hash of the packed sequence bytes.
-    pub fn seq_hash(&self) -> u64 {
-        xxh3_64(&self.seq)
-    }
 }
 
 struct SKKmerIter<'a> {