feat: enhance memory budgeting and add rebuild diagnostics

This commit improves memory management by respecting Linux cgroup v1/v2 limits and introduces a configurable memory budget for the new `rebuild` subcommand to prevent OOM during index reconstruction. The rebuild process now supports filtering, compaction, and parallelization. Diagnostic capabilities are expanded with debug-level tracing for partition merges, k-mer expansion tracking, and utility flags for label renaming, matrix size breakdowns, per-genome counts, and partition distribution reporting. Accessor methods for active and remaining memory have also been added to the stats struct.

src/obikindex/src/merge.rs

@@ -7,7 +7,7 @@ use std::sync::{Arc, Mutex};
 
 use obisys::{MemoryBudget, Reporter, Stage, available_memory_bytes, progress_bar, spinner};
 use rayon::prelude::*;
-use tracing::info;
+use tracing::{debug, info};
 
 use obilayeredmap::IndexMode;
 
@@ -250,6 +250,15 @@ impl KmerIndex {
                     let cost   = ubytes * exp / 1000;
 
                     budget.acquire(cost);
+                    debug!(
+                        "partition {i}: start — est. {} ({:.2}×), \
+                         {} workers active, {} budget remaining",
+                        fmt_bytes(cost),
+                        exp as f64 / 1000.0,
+                        budget.active(),
+                        fmt_bytes(budget.remaining()),
+                    );
+
                     let result = dst_partition
                         .merge_partition(i, &srcs, mode, n_dst_genomes, block_bits, &evidence);
                     budget.release(cost);
@@ -257,10 +266,19 @@ impl KmerIndex {
 
                     match result {
                         Ok(g_len) => {
-                            if ubytes > 0 {
-                                let actual = g_len as u64 * 16 * 1000 / ubytes;
-                                max_expansion.fetch_max(actual, Ordering::Relaxed);
-                            }
+                            let actual_exp = if ubytes > 0 {
+                                g_len as u64 * 16 * 1000 / ubytes
+                            } else {
+                                0
+                            };
+                            max_expansion.fetch_max(actual_exp, Ordering::Relaxed);
+                            debug!(
+                                "partition {i}: done — {} new kmers, actual {:.2}× \
+                                 (estimated {:.2}×)",
+                                g_len,
+                                actual_exp as f64 / 1000.0,
+                                exp as f64 / 1000.0,
+                            );
                             part_stats.lock().unwrap().push(PartStat {
                                 id:             i,
                                 unitig_bytes:   ubytes,