diff --git a/sbysrc/sby_core.py b/sbysrc/sby_core.py
index 2d0d1c2..17b1ae9 100644
--- a/sbysrc/sby_core.py
+++ b/sbysrc/sby_core.py
@@ -45,12 +45,8 @@ signal.signal(signal.SIGINT, force_shutdown)
 signal.signal(signal.SIGTERM, force_shutdown)
 
 def process_filename(filename):
-    if filename.startswith("~/"):
-        filename = os.environ['HOME'] + filename[1:]
-
     filename = os.path.expandvars(filename)
-
-    return filename
+    return Path(filename).expanduser()
 
 def dress_message(workdir, logmessage):
     tm = localtime()
@@ -579,7 +575,7 @@ class SbyConfig:
                     self.error(f"sby file syntax error: '[files]' section entry expects up to 2 arguments, {len(entries)} specified")
 
                 if len(entries) == 1:
-                    self.files[os.path.basename(entries[0])] = entries[0]
+                    self.files[Path(entries[0]).name] = entries[0]
                 elif len(entries) == 2:
                     self.files[entries[0]] = entries[1]
 
@@ -1033,42 +1029,44 @@ class SbyTask(SbyConfig):
         raise SbyAbort(logmessage)
 
     def makedirs(self, path):
-        if self.reusedir and os.path.isdir(path):
+        path = Path(path)
+        if self.reusedir and path.is_dir():
             rmtree(path, ignore_errors=True)
-        if not os.path.isdir(path):
-            os.makedirs(path)
+        path.mkdir(parents=True, exist_ok=True)
 
     def copy_src(self, linkmode=False):
-        self.makedirs(self.workdir + "/src")
+        outdir = Path(self.workdir) / "src"
+        self.makedirs(outdir)
 
         for dstfile, lines in self.verbatim_files.items():
-            dstfile = self.workdir + "/src/" + dstfile
-            self.log(f"Writing '{dstfile}'.")
+            dstfile = outdir / dstfile
+            self.log(f"Writing '{dstfile.absolute()}'.")
+            dstfile.parent.mkdir(parents=True, exist_ok=True)
 
             with open(dstfile, "w") as f:
                 for line in lines:
                     f.write(line)
 
         for dstfile, srcfile in self.files.items():
-            if dstfile.startswith("/") or dstfile.startswith("../") or ("/../" in dstfile):
+            dstfile = Path(dstfile)
+            if dstfile.is_absolute() or ".." in dstfile.parts:
                 self.error(f"destination filename must be a relative path without /../: {dstfile}")
-            dstfile = self.workdir + "/src/" + dstfile
+            dstfile = outdir / dstfile
 
             srcfile = process_filename(srcfile)
 
-            basedir = os.path.dirname(dstfile)
-            if basedir != "" and not os.path.exists(basedir):
-                os.makedirs(basedir)
+            basedir = dstfile.parent
+            basedir.mkdir(parents=True, exist_ok=True)
 
             if linkmode:
                 verb = "Link"
             else:
                 verb = "Copy"
-            self.log(f"{verb} '{os.path.abspath(srcfile)}' to '{os.path.abspath(dstfile)}'.")
+            self.log(f"{verb} '{srcfile.absolute()}' to '{dstfile.absolute()}'.")
 
             if linkmode:
-                os.symlink(os.path.relpath(srcfile, basedir), dstfile)
-            elif os.path.isdir(srcfile):
+                os.symlink(srcfile.resolve(), dstfile)
+            elif srcfile.is_dir():
                 copytree(srcfile, dstfile, dirs_exist_ok=True)
             else:
                 copyfile(srcfile, dstfile)
@@ -1097,12 +1095,12 @@ class SbyTask(SbyConfig):
             self.__dict__["opt_" + option_name] = default_value
 
     def make_model(self, model_name):
-        if not os.path.isdir(f"{self.workdir}/model"):
-            os.makedirs(f"{self.workdir}/model")
+        modeldir = Path(self.workdir) / "model"
+        modeldir.mkdir(exist_ok=True)
 
         if model_name == "prep":
-            with open(f"""{self.workdir}/model/design_prep.ys""", "w") as f:
-                print(f"# running in {self.workdir}/model/", file=f)
+            with open(modeldir / "design_prep.ys", "w") as f:
+                print(f"# running in {modeldir}/", file=f)
                 print(f"""read_rtlil design.il""", file=f)
                 if not self.opt_skip_prep:
                     print("scc -select; simplemap; select -clear", file=f)
@@ -1146,7 +1144,7 @@ class SbyTask(SbyConfig):
             return [proc]
 
         if model_name == "base":
-            with open(f"""{self.workdir}/model/design.ys""", "w") as f:
+            with open(modeldir / "design.ys", "w") as f:
                 print(f"# running in {self.workdir}/src/", file=f)
                 for cmd in self.script:
                     print(cmd, file=f)
@@ -1168,7 +1166,7 @@ class SbyTask(SbyConfig):
 
             def instance_hierarchy_callback(retcode):
                 if self.design == None:
-                    with open(f"{self.workdir}/model/design.json") as f:
+                    with open(modeldir / "design.json") as f:
                         self.design = design_hierarchy(f)
                         self.status_db.create_task_properties([
                             prop for prop in self.design.properties_by_path.values()
@@ -1184,8 +1182,8 @@ class SbyTask(SbyConfig):
             return [proc]
 
         if re.match(r"^smt2(_syn)?(_nomem)?(_stbv|_stdt)?$", model_name):
-            with open(f"{self.workdir}/model/design_{model_name}.ys", "w") as f:
-                print(f"# running in {self.workdir}/model/", file=f)
+            with open(modeldir / f"design_{model_name}.ys", "w") as f:
+                print(f"# running in {modeldir}/", file=f)
                 print(f"""read_rtlil design_prep.il""", file=f)
                 print("hierarchy -smtcheck", file=f)
                 print("delete */t:$print", file=f)
@@ -1218,8 +1216,8 @@ class SbyTask(SbyConfig):
             return [proc]
 
         if re.match(r"^btor(_syn)?(_nomem)?$", model_name):
-            with open(f"{self.workdir}/model/design_{model_name}.ys", "w") as f:
-                print(f"# running in {self.workdir}/model/", file=f)
+            with open(modeldir / f"design_{model_name}.ys", "w") as f:
+                print(f"# running in {modeldir}/", file=f)
                 print(f"""read_rtlil design_prep.il""", file=f)
                 print("hierarchy -simcheck", file=f)
                 print("delete */t:$print", file=f)
@@ -1254,8 +1252,8 @@ class SbyTask(SbyConfig):
             return [proc]
 
         if model_name == "aig":
-            with open(f"{self.workdir}/model/design_aiger.ys", "w") as f:
-                print(f"# running in {self.workdir}/model/", file=f)
+            with open(modeldir / "design_aiger.ys", "w") as f:
+                print(f"# running in {modeldir}/", file=f)
                 print("read_rtlil design_prep.il", file=f)
                 print("delete */t:$print", file=f)
                 print("hierarchy -simcheck", file=f)
@@ -1281,7 +1279,7 @@ class SbyTask(SbyConfig):
                 self,
                 "aig",
                 self.model("prep"),
-                f"""cd {self.workdir}/model; {self.exe_paths["yosys"]} -ql design_aiger.log design_aiger.ys"""
+                f"""cd {modeldir}; {self.exe_paths["yosys"]} -ql design_aiger.log design_aiger.ys"""
             )
             proc.checkretcode = True
 
@@ -1292,8 +1290,8 @@ class SbyTask(SbyConfig):
                 self,
                 model_name,
                 self.model("aig"),
-                f"""cd {self.workdir}/model; {self.exe_paths["abc"]} -c 'read_aiger design_aiger.aig; fold{" -s" if self.opt_aigfolds else ""}; strash; write_aiger design_aiger_fold.aig'""",
-                logfile=open(f"{self.workdir}/model/design_aiger_fold.log", "w")
+                f"""cd {modeldir}; {self.exe_paths["abc"]} -c 'read_aiger design_aiger.aig; fold{" -s" if self.opt_aigfolds else ""}; strash; write_aiger design_aiger_fold.aig'""",
+                logfile=open(f"{modeldir}/design_aiger_fold.log", "w")
             )
             proc.checkretcode = True
 
diff --git a/tests/links/more_dirs.sby b/tests/links/more_dirs.sby
new file mode 100644
index 0000000..9a926dd
--- /dev/null
+++ b/tests/links/more_dirs.sby
@@ -0,0 +1,20 @@
+[tasks]
+link
+copy
+
+[options]
+mode prep
+
+[engines]
+btor btormc
+
+[script]
+read -noverific
+script dir/script.ys
+
+[files]
+here/dir ${WORKDIR}/../dir
+a/b/c.v prv32fmcmp.v
+
+[file here/doc]
+log foo
diff --git a/tests/links/more_dirs.sh b/tests/links/more_dirs.sh
new file mode 100644
index 0000000..aa9ce11
--- /dev/null
+++ b/tests/links/more_dirs.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+set -e
+if [[ $TASK == link ]]; then
+    flags="--setup --link"
+else
+    flags="--setup"
+fi
+python3 $SBY_MAIN -f $SBY_FILE $TASK $flags
+
+test -e ${WORKDIR}/src/here/dir -a -e ${WORKDIR}/src/a/b/c.v -a -e ${WORKDIR}/src/here/doc
diff --git a/tests/links/symlink.py b/tests/links/symlink.py
index a6a06d5..f274d61 100644
--- a/tests/links/symlink.py
+++ b/tests/links/symlink.py
@@ -1,10 +1,10 @@
-import os
 from pathlib import Path
 import sys
 
 def main():
     workdir, task = sys.argv[1:]
     src = Path(workdir) / "src"
+    count = 0
     for srcfile in src.iterdir():
         if srcfile.name == "heredoc":
             assert(not srcfile.is_symlink())
@@ -13,6 +13,11 @@ def main():
                 assert(local_contents.strip() == 'log foo')
         else:
             assert(srcfile.is_symlink() == (task == "link"))
+            assert(srcfile.name != "script.ys")
+        count += 1
+    assert(count == 4)
+    script_ys = src / "dir" / "script.ys"
+    assert(script_ys.exists())
 
 if __name__ == "__main__":
     main()
diff --git a/tests/links/symlink.sby b/tests/links/symlink.sby
index 52fa881..c3841ce 100644
--- a/tests/links/symlink.sby
+++ b/tests/links/symlink.sby
@@ -1,6 +1,8 @@
 [tasks]
 link
 copy
+dir_implicit: dir
+dir_explicit: dir
 
 [options]
 mode prep
@@ -15,7 +17,9 @@ script dir/script.ys
 [files]
 ../../docs/examples/demos/picorv32.v
 prv32fmcmp.v
-dir
+~dir: dir
+dir_implicit: dir/
+dir_explicit: dir/ dir/
 
 [file heredoc]
 log foo