diff --git a/tests/run-prune.bats b/tests/run-prune.bats
new file mode 100644
index 0000000..af2c5ca
--- /dev/null
+++ b/tests/run-prune.bats
@@ -0,0 +1,68 @@
+#!/usr/bin/env bats
+# tests/run-prune.bats — prune orphaned sources (no LLM, no network; DRY_RUN).
+setup() {
+  load 'helpers'
+  export PRUNE="${SKILL_SCRIPTS}/run-prune.sh"
+  export GENOMES_ROOT="${BATS_TEST_TMPDIR}"
+  export INGEST_BASE="main"
+  export KG_LIB_DIR="${LIB_DIR}"
+  export FORGEJO_URL="http://forgejo.local" FORGEJO_USER="u" FORGEJO_TOKEN="t"
+  export DRY_RUN=1
+  g_src="$(make_fixture_genome)"; export g_name="fixture-genome"
+  mv "$g_src" "${GENOMES_ROOT}/${g_name}"; export g="${GENOMES_ROOT}/${g_name}"
+  ( cd "$g" && rm -f raw/articles/test.md && git add -A && git commit -q -m clear && git push -q )
+}
+
+@test "run-prune: removes only the orphaned source + its index entry, opens a dry PR" {
+  command -v jq >/dev/null 2>&1 || skip "jq not installed"
+  cd "$g"
+  # kept: raw exists. orphan: raw missing.
+  echo content > raw/articles/kept.md
+  h="$(sha256sum raw/articles/kept.md | cut -d' ' -f1)"
+  printf -- '---\nsource_path: raw/articles/kept.md\nsource_sha256: %s\n---\nbody\n' "$h" > wiki/sources/kept.md
+  printf -- '---\nsource_path: raw/articles/gone.md\nsource_sha256: abc\n---\nbody\n' > wiki/sources/orphan.md
+  python3 "$SKILL_SCRIPTS/index-append.py" --section Sources --entry '- [[sources/kept]] — kept. `maturity: draft`'
+  python3 "$SKILL_SCRIPTS/index-append.py" --section Sources --entry '- [[sources/orphan]] — orphan. `maturity: draft`'
+  git add -A && git commit -q -m setup && git push -q
+
+  run bash "$PRUNE" "$g_name"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *'"status":"ok"'* ]]
+  [[ "$output" == *'"count":1'* ]]
+
+  # only the orphan page is gone
+  [ ! -f wiki/sources/orphan.md ]
+  [ -f wiki/sources/kept.md ]
+  # index reflects the removal
+  ! grep -q 'sources/orphan' wiki/index.md
+  grep -q 'sources/kept' wiki/index.md
+  # committed on a chore/ branch (NOT feat/ai-ingest-*)
+  git rev-parse --verify "chore/prune-orphans-$(date +%F)"
+}
+
+@test "run-prune: no orphans -> count 0 and no PR/branch" {
+  command -v jq >/dev/null 2>&1 || skip "jq not installed"
+  cd "$g"
+  echo content > raw/articles/kept.md
+  h="$(sha256sum raw/articles/kept.md | cut -d' ' -f1)"
+  printf -- '---\nsource_path: raw/articles/kept.md\nsource_sha256: %s\n---\nbody\n' "$h" > wiki/sources/kept.md
+  git add -A && git commit -q -m setup && git push -q
+
+  run bash "$PRUNE" "$g_name"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *'"count":0'* ]]
+  run git rev-parse --verify "chore/prune-orphans-$(date +%F)"
+  [ "$status" -ne 0 ]
+}
+
+@test "run-prune: refuses when an orphan path would escape wiki/ (defense in depth)" {
+  command -v jq >/dev/null 2>&1 || skip "jq not installed"
+  cd "$g"
+  # legacy page without source_path is ignored; a page with a missing raw is the orphan.
+  printf -- '---\nsource_path: raw/articles/gone.md\nsource_sha256: abc\n---\nbody\n' > wiki/sources/orphan.md
+  git add -A && git commit -q -m setup && git push -q
+  run bash "$PRUNE" "$g_name"
+  [ "$status" -eq 0 ]
+  [[ "$output" == *'"count":1'* ]]
+  [ ! -f wiki/sources/orphan.md ]
+}