fix: tool bugs found in review audit

repl:  env var was dead code (hardcoded 2s), empty frame gave misleading error
check-tangle: show full SBCL output on compile failure, not filtered
verify-repl: blacklist now configurable via VERIFY_REPL_EXCLUDE env var;
  regex tightened to ';; +REPL-VERIFIED:' from ';;.REPL.VERIFIED:' (ambiguous)
org-eval: 1-based indexing to match repl-block; errors on out-of-range; errors on <1

projects/check-tangle/check-tangle

@@ -69,7 +69,7 @@ if echo "$OUTPUT" | grep -q ":OK"; then
     echo "OK: $ORG_FILE compiles cleanly" >&2
     exit 0
 else
-    echo "$OUTPUT" | grep -v '^;' | grep -v '^$' | head -5
     echo "FAIL: $ORG_FILE — compilation error" >&2
+    echo "$OUTPUT"
     exit 1
 fi

projects/org-eval-tool/org-eval

@@ -1,14 +1,16 @@
 #!/usr/bin/env bash
 # Evaluate an org src block using Emacs batch mode
 # Usage: org-eval <org-file> [block-index]
-# If block-index is not provided, evaluates all blocks
+#   block-index is 1-based (first block = 1).
+#   If omitted, evaluates ALL blocks.
 
 set -e
 
 if [ $# -lt 1 ]; then
     echo "Usage: org-eval <org-file> [block-index]"
     echo "  Evaluates src blocks in the org file"
-    echo "  If block-index is omitted, evaluates ALL blocks"
+    echo "  block-index is 1-based (first block = 1)"
+    echo "  If omitted, evaluates ALL blocks"
     exit 1
 fi
 
@@ -23,15 +25,23 @@ fi
 echo "Evaluating: $ORG_FILE"
 
 if [ -n "$BLOCK_INDEX" ]; then
+    # 1-based indexing: subtract 1 for Emacs' dotimes (0-based)
+    if [ "$BLOCK_INDEX" -lt 1 ]; then
+        echo "Error: block-index must be 1 or greater" >&2
+        exit 1
+    fi
+    SKIP=$((BLOCK_INDEX - 1))
     # Evaluate specific block
     emacs --batch \
         --load org \
         --eval "(setq org-confirm-babel-evaluate nil)" \
         --eval "(with-current-buffer (find-file-noselect \"$ORG_FILE\") \
                  (goto-char (point-min)) \
-                 (dotimes (_ $BLOCK_INDEX) \
+                 (dotimes (_ $SKIP) \
                    (org-babel-next-src-block)) \
-                 (org-babel-execute-src-block))"
+                 (if (org-in-src-block-p t) \
+                     (org-babel-execute-src-block) \
+                   (error \"Block $BLOCK_INDEX not found\")))"
 else
     # Evaluate all blocks
     emacs --batch \

projects/repl-tool/repl

@@ -30,7 +30,7 @@ my $sock = IO::Socket::INET->new(
     PeerHost  => $HOST,
     PeerPort  => $PORT,
     Proto     => "tcp",
-    Timeout   => 2
+    Timeout   => $TIMEOUT
 ) or die "Cannot connect to $HOST:$PORT: $!\n";
 
 sub read_frame {
@@ -58,7 +58,11 @@ write_frame($sock, $msg);
 
 # Read response
 my $response = read_frame($sock);
-if ($response) {
+if (defined $response) {
+    if ($response eq "") {
+        print STDERR "Daemon returned empty response\n";
+        exit 1;
+    }
     if ($response =~ /:VALUE "([^"]*)"/s) {
         print "$1\n";
     } elsif ($response =~ /:message "([^"]*)"/s) {

projects/verify-repl-tool/verify-repl

@@ -22,7 +22,9 @@ VIOLATIONS=0
 FILES_CHECKED=0
 
 # Blacklist: files exempt from REPL verification (core infrastructure, tests)
-BLACKLIST=(
+# Override with $VERIFY_REPL_EXCLUDE (space-separated filenames).
+# Example: VERIFY_REPL_EXCLUDE="setup.org package.lisp" verify-repl org/
+DEFAULT_BLACKLIST=(
     "core-defpackage.org"
     "core-manifest.org"
     "core-skills.org"
@@ -31,6 +33,12 @@ BLACKLIST=(
     "setup.org"
 )
 
+if [ -n "${VERIFY_REPL_EXCLUDE:-}" ]; then
+    IFS=' ' read -ra BLACKLIST <<< "$VERIFY_REPL_EXCLUDE"
+else
+    BLACKLIST=("${DEFAULT_BLACKLIST[@]}")
+fi
+
 is_blacklisted() {
     local fname
     fname=$(basename "$1")
@@ -75,7 +83,8 @@ check_file() {
             def_count=0
             has_repl_verify=0
             # Check for REPL-VERIFIED comment on previous line(s)
-            if echo "$prev_line" | grep -qE ';;.REPL.VERIFIED:'; then
+            # Matches ";; REPL-VERIFIED:" or ";;  REPL-VERIFIED:" etc.
+            if echo "$prev_line" | grep -qE ';; +REPL[-_]VERIFIED:'; then
                 has_repl_verify=1
             fi
             # Check for prose requirement: was there a headline before this block?