diff --git a/dv/uvm/core_ibex/scripts/merge_cov.py b/dv/uvm/core_ibex/scripts/merge_cov.py
index 35e26fed67..79585f3887 100755
--- a/dv/uvm/core_ibex/scripts/merge_cov.py
+++ b/dv/uvm/core_ibex/scripts/merge_cov.py
@@ -39,15 +39,23 @@ def find_cov_dbs(start_dir: pathlib.Path, simulator: str) -> Set[pathlib.Path]:
 
 
 def merge_cov_vcs(md: RegressionMetadata, cov_dirs: Set[pathlib.Path]) -> int:
-    logging.info("Generating merged coverage directory")
     cmd = (['urg', '-full64',
             '-format', 'both',
-            '-dbname', str(md.cov_dir/'merged.vdb'),
-            '-report', str(md.cov_dir/'report'),
-            '-log', str(md.cov_dir/'merge.log'),
+            '-dbname', str(md.dir_cov/'merged.vdb'),
+            '-report', str(md.dir_cov/'report'),
+            '-log', str(md.dir_cov/'merge.log'),
             '-dir'] +
-           list(cov_dirs))
-    return run_one(md.verbose, cmd, redirect_stdstreams='/dev/null')
+          list(map(str, cov_dirs)))
+
+    # Update the metdadata file with the commands we're about to run
+    with LockedMetadata(md.dir_metadata, __file__) as md:
+        md.cov_merge_log = md.dir_cov / 'merge.log'
+        md.cov_merge_stdout = md.dir_cov / 'merge.log.stdout'
+        md.cov_merge_cmds = [cmd]
+
+        with open(md.cov_merge_stdout, 'wb') as fd:
+            logging.info("Generating merged coverage directory")
+            return run_one(md.verbose, cmd, redirect_stdstreams=fd)
 
 
 def merge_cov_xlm(md: RegressionMetadata, cov_dbs: Set[pathlib.Path]) -> int:
diff --git a/dv/uvm/core_ibex/scripts/run_rtl.py b/dv/uvm/core_ibex/scripts/run_rtl.py
index 8334a94155..cc5d9de323 100755
--- a/dv/uvm/core_ibex/scripts/run_rtl.py
+++ b/dv/uvm/core_ibex/scripts/run_rtl.py
@@ -67,6 +67,7 @@ def _main() -> int:
         'rtl_sim_log': trr.rtl_log,
         'rtl_trace': trr.rtl_trace.parent/'trace_core',
         'iss_cosim_trace': trr.iss_cosim_trace,
+        'core_ibex': md.ibex_dv_root,
         'sim_opts': (f"+signature_addr={md.signature_addr}\n" +
                      f"+test_timeout_s={trr.timeout_s}\n" +
                      f"{get_sim_opts(md.ibex_config, md.simulator)}\n" +
diff --git a/dv/uvm/core_ibex/yaml/rtl_simulation.yaml b/dv/uvm/core_ibex/yaml/rtl_simulation.yaml
index a18b8a5725..490f613923 100644
--- a/dv/uvm/core_ibex/yaml/rtl_simulation.yaml
+++ b/dv/uvm/core_ibex/yaml/rtl_simulation.yaml
@@ -51,7 +51,6 @@
     wave_opts: >-
       -debug_access+all
       -ucli
-      -do vcs.tcl
     cosim_opts: >-
       -f <core_ibex>/ibex_dv_cosim_dpi.f
       -LDFLAGS '<ISS_LDFLAGS>'
@@ -81,7 +80,7 @@
       +enable_ibex_fcov=1
     wave_opts: >
       -ucli
-      -do <cwd>/vcs.tcl
+      -do <core_ibex>/vcs.tcl
 
 
 ############################################################