fix: SPDX header positioning, remove 4 remaining silent catches

- Move SPDX headers to line 1 in 11 files (was buried in comment blocks)
- Remove duplicate SPDX block in reextract.zig
- Fix 4 remaining catch {} blocks: prefetch ring submit, dragonfly
  socket timeouts, stages write — all now log errors
- All @ptrCast/@aligncast already have // SAFETY: comments

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: hyperpolymath

ffi/zig/src/cache.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl Cache — LMDB-Backed Result Cache
 //
 // Stores parsed document results keyed by file path. On cache hit
@@ -17,9 +19,6 @@
 //
 // Each Chapel locale should have its own LMDB environment to avoid
 // cross-locale write locking. Reads are fully concurrent.
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 

ffi/zig/src/capnp.zig

@@ -1,13 +1,12 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — Minimal Cap'n Proto Single-Segment Message Builder
 //
 // Produces valid Cap'n Proto binary messages readable by any standard decoder.
 // Single-segment only (sufficient for per-document stage results).
 // No external dependencies — pure Zig implementation of the wire format.
 //
 // Wire format reference: https://capnproto.org/encoding.html
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 

ffi/zig/src/conduit.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — Preprocessing Conduit
 //
 // Lightweight pre-processing pipeline that runs before the main Chapel parse.
@@ -11,9 +13,6 @@
 // Chapel calls ddac_conduit_process() on a batch of paths. The conduit
 // returns an array of ConduitResult structs that the main loop uses to
 // skip invalid files and pre-populate cache keys.
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 

ffi/zig/src/docudactyl_ffi.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl FFI — Unified Multi-Format Parser Dispatcher
 //
 // Thin Zig wrapper around C libraries for HPC document processing.
@@ -11,9 +13,6 @@
 //   - libxml2          (EPUB/XHTML parsing)
 //   - libgdal          (geospatial: shapefiles, GeoTIFF)
 //   - libvips          (image dimensions/metadata)
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 const stages = @import("stages.zig");

ffi/zig/src/dragonfly.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — Dragonfly / Redis RESP Client (L2 Cache)
 //
 // Minimal RESP2 client for Dragonfly (Redis-compatible) cross-locale cache.
@@ -10,9 +12,6 @@
 //   - 25x throughput on same hardware
 //   - Multi-threaded (no single-thread bottleneck)
 //   - Compatible with RESP2 protocol
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 
@@ -41,9 +40,15 @@ pub const DragonflyClient = struct {
         const addr = std.net.Address.parseIp4(host, port) catch return null;
         const stream = std.net.tcpConnectToAddress(addr) catch return null;
 
-        // Set a reasonable timeout (5 seconds)
-        stream.handle.setReadTimeout(5_000_000_000) catch {};
-        stream.handle.setWriteTimeout(5_000_000_000) catch {};
+        // Set a reasonable timeout (5 seconds). Failure to set timeouts is
+        // non-fatal — operations will block indefinitely on network stalls,
+        // but the connection itself is still usable.
+        stream.handle.setReadTimeout(5_000_000_000) catch |err| {
+            std.log.debug("Dragonfly: failed to set read timeout: {s}", .{@errorName(err)});
+        };
+        stream.handle.setWriteTimeout(5_000_000_000) catch |err| {
+            std.log.debug("Dragonfly: failed to set write timeout: {s}", .{@errorName(err)});
+        };
 
         return .{
             .stream = stream,

ffi/zig/src/gpu_ocr.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — GPU-Accelerated OCR Coprocessor
 //
 // Batched OCR using GPU acceleration when available:
@@ -16,9 +18,6 @@
 // and collects results via ddac_gpu_ocr_collect(). The coprocessor maintains
 // an internal queue and flushes batches to the GPU when full or on explicit
 // flush.
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 

ffi/zig/src/hw_crypto.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — Hardware Crypto Acceleration
 //
 // Detects and leverages hardware SHA-256 instructions for maximum throughput
@@ -14,9 +16,6 @@
 //   - Multi-buffer SHA-256 for batch operations (4 files at once with AVX2)
 //   - Runtime capability reporting for Chapel banner
 //   - Batch digest computation for the conduit pipeline
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 

ffi/zig/src/lith_adapter.zig

@@ -1,14 +1,13 @@
-// Docudactyl → Lithoglyph Ingest Adapter
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
+// Docudactyl — Lithoglyph Ingest Adapter
 //
 // Reads a Cap'n Proto StageResults message buffer and converts it to a JSON
 // evidence record compatible with Lithoglyph's bofig_evidence schema.
 //
 // The adapter extracts fields from the Cap'n Proto binary layout defined in
 // capnp.zig, maps them to Lithoglyph schema fields, and computes auto-PROMPT
 // epistemological scores from extraction metadata.
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 const capnp = @import("capnp.zig");

ffi/zig/src/ml_inference.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — ML Inference Engine (ONNX Runtime)
 //
 // Unified ML inference backend for all ML-dependent processing stages:
@@ -19,9 +21,6 @@
 // use (lazy loading) and caches the ONNX session for subsequent calls.
 //
 // Model paths are configured via ddac_ml_set_model_dir().
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 

ffi/zig/src/prefetch.zig

@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 // Docudactyl — I/O Prefetcher (Linux io_uring + fadvise)
 //
 // Addresses Wall 2 (I/O bandwidth) by prefetching upcoming documents
@@ -10,9 +12,6 @@
 // The prefetcher manages a sliding window of N upcoming files.
 // Chapel tasks call ddac_prefetch_hint() before processing each document
 // to keep the pipeline full.
-//
-// SPDX-License-Identifier: PMPL-1.0-or-later
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
 
 const std = @import("std");
 const builtin = @import("builtin");
@@ -182,8 +181,11 @@ fn prefetchWithUring(state: *PrefetchState, fd: std.posix.fd_t) void {
         sqe.prep_fadvise(fd, 0, @intCast(READAHEAD_SIZE), 3); // POSIX_FADV_WILLNEED
         sqe.user_data = @intCast(fd);
 
-        // Submit without waiting
-        _ = ring_state.ring.submit() catch {};
+        // Submit without waiting — failure is non-fatal; the file will still
+        // be read synchronously when the parser reaches it.
+        _ = ring_state.ring.submit() catch |err| {
+            std.log.debug("io_uring prefetch submit failed: {s}", .{@errorName(err)});
+        };
     }
 }