diff --git a/.github/workflows/eval-pr-run.yml b/.github/workflows/eval-pr-run.yml
index b2a7b7dd..c64dbfe4 100644
--- a/.github/workflows/eval-pr-run.yml
+++ b/.github/workflows/eval-pr-run.yml
@@ -72,7 +72,6 @@ jobs:
               return;
             }
             core.setOutput('pr_number', pr.number.toString());
-            core.setOutput('base_sha', pr.base.sha);
             core.setOutput('author', pr.user.login);
 
             let trusted = false;
@@ -98,9 +97,8 @@ jobs:
 
       - name: Discover changed skills
         id: discover
-        env:
-          BASE_SHA: ${{ steps.pr.outputs.base_sha }}
         run: |
+          BASE_SHA=$(git rev-parse HEAD^1)
           changed_files=$(git diff --name-only "$BASE_SHA"...HEAD)
           echo "Changed files:"
           echo "$changed_files"
diff --git a/tests/test-skill-discovery.sh b/tests/test-skill-discovery.sh
new file mode 100755
index 00000000..b1b2217f
--- /dev/null
+++ b/tests/test-skill-discovery.sh
@@ -0,0 +1,130 @@
+#!/usr/bin/env bash
+# Reproducer test for TC-5101 / TC-5102: verifies that the eval-pr-run
+# skill discovery script detects only PR-changed skills, not files
+# introduced on main after the PR branch forked.
+set -euo pipefail
+
+WORK_DIR=$(mktemp -d)
+trap 'rm -rf "$WORK_DIR"' EXIT
+
+pass=0
+fail=0
+
+assert_eq() {
+  local label="$1" expected="$2" actual="$3"
+  if [ "$expected" = "$actual" ]; then
+    echo "  PASS: $label"
+    pass=$((pass + 1))
+  else
+    echo "  FAIL: $label"
+    echo "    expected: $expected"
+    echo "    actual:   $actual"
+    fail=$((fail + 1))
+  fi
+}
+
+# --- Setup: create a repo mimicking refs/pull/N/merge topology ---
+
+cd "$WORK_DIR"
+git init -q repo && cd repo
+git config user.email "test@test.com"
+git config user.name "Test"
+
+# Initial commit on main with skill and eval structures
+mkdir -p plugins/sdlc-workflow/skills/{alpha,beta,gamma}
+mkdir -p evals/{alpha,beta,gamma}
+for s in alpha beta gamma; do
+  echo "skill $s" > "plugins/sdlc-workflow/skills/$s/SKILL.md"
+  echo '{"evals":[]}' > "evals/$s/evals.json"
+done
+git add -A && git commit -q -m "init: add skills alpha, beta, gamma"
+
+# Record the fork point (this is what pr.base.sha would return)
+FORK_POINT=$(git rev-parse HEAD)
+
+# Create the PR branch from this point
+git checkout -q -b pr-branch
+
+# PR changes only the "alpha" skill
+echo "updated alpha" > plugins/sdlc-workflow/skills/alpha/SKILL.md
+git add -A && git commit -q -m "pr: update alpha skill"
+PR_HEAD=$(git rev-parse HEAD)
+
+# Switch back to main and add a baseline commit touching ALL skills
+git checkout -q main
+for s in alpha beta gamma; do
+  mkdir -p "evals/$s/baselines/abc123"
+  echo "baseline" > "evals/$s/baselines/abc123/benchmark.json"
+done
+git add -A && git commit -q -m "chore(evals): create baselines for all skills"
+MAIN_TIP=$(git rev-parse HEAD)
+
+# Create a merge commit mimicking refs/pull/N/merge
+git merge -q --no-ff pr-branch -m "Merge PR into main"
+
+# --- Extract the discovery script from the workflow ---
+
+discover() {
+  local base_sha="$1"
+  local changed_files
+  changed_files=$(git diff --name-only "$base_sha"...HEAD)
+
+  local skills=""
+  for file in $changed_files; do
+    local skill=""
+    if [[ "$file" =~ ^plugins/sdlc-workflow/skills/([^/]+)/ ]]; then
+      skill="${BASH_REMATCH[1]}"
+    elif [[ "$file" =~ ^evals/([^/]+)/ ]]; then
+      skill="${BASH_REMATCH[1]}"
+    fi
+
+    if [ -n "$skill" ] && [ -f "evals/${skill}/evals.json" ]; then
+      if [[ ! ",$skills," == *",$skill,"* ]]; then
+        skills="${skills:+${skills},}${skill}"
+      fi
+    fi
+  done
+  echo "$skills"
+}
+
+# --- Test 1: OLD approach (pr.base.sha = fork point) detects too many skills ---
+echo "Test 1: Old approach (stale pr.base.sha) over-detects"
+old_result=$(discover "$FORK_POINT")
+# Sort for stable comparison
+old_sorted=$(echo "$old_result" | tr ',' '\n' | sort | tr '\n' ',' | sed 's/,$//')
+assert_eq "detects all three skills (bug)" "alpha,beta,gamma" "$old_sorted"
+
+# --- Test 2: NEW approach (HEAD^1 = merge commit first parent) detects only PR skills ---
+echo "Test 2: New approach (HEAD^1) detects only changed skill"
+MERGE_PARENT=$(git rev-parse HEAD^1)
+new_result=$(discover "$MERGE_PARENT")
+assert_eq "detects only alpha" "alpha" "$new_result"
+
+# --- Test 3: skill changes via evals/ path are also detected ---
+echo "Test 3: Eval file changes detected via evals/ regex"
+git checkout -q -b pr-branch-2 main
+echo '{"evals":[{"name":"test"}]}' > evals/beta/evals.json
+git add -A && git commit -q -m "pr: update beta evals"
+git checkout -q main
+git merge -q --no-ff pr-branch-2 -m "Merge PR 2 into main"
+MERGE_PARENT_2=$(git rev-parse HEAD^1)
+result_3=$(discover "$MERGE_PARENT_2")
+assert_eq "detects only beta" "beta" "$result_3"
+
+# --- Test 4: skill changes under plugins/ path are detected ---
+echo "Test 4: Skill file changes detected via plugins/ regex"
+git checkout -q -b pr-branch-3 main
+echo "new content" > plugins/sdlc-workflow/skills/gamma/SKILL.md
+git add -A && git commit -q -m "pr: update gamma skill"
+git checkout -q main
+git merge -q --no-ff pr-branch-3 -m "Merge PR 3 into main"
+MERGE_PARENT_3=$(git rev-parse HEAD^1)
+result_4=$(discover "$MERGE_PARENT_3")
+assert_eq "detects only gamma" "gamma" "$result_4"
+
+# --- Summary ---
+echo ""
+echo "Results: $pass passed, $fail failed"
+if [ "$fail" -gt 0 ]; then
+  exit 1
+fi