diff --git a/infer/src/backend/infer.ml b/infer/src/backend/infer.ml
index 5ef1b8763..2ae0d9f84 100644
--- a/infer/src/backend/infer.ml
+++ b/infer/src/backend/infer.ml
@@ -144,7 +144,8 @@ let check_xcpretty () =
       exit 1
 
 let capture_with_compilation_database db_files =
-  Config.clang_compilation_db_files := IList.map Utils.filename_to_absolute db_files;
+  let root = Unix.getcwd () in
+  Config.clang_compilation_db_files := IList.map (Utils.filename_to_absolute ~root) db_files;
   let compilation_database = CompilationDatabase.from_json_files db_files in
   CaptureCompilationDatabase.capture_files_in_database compilation_database
 
diff --git a/infer/src/base/CommandLineOption.ml b/infer/src/base/CommandLineOption.ml
index dc5bcda9e..d4fc82558 100644
--- a/infer/src/base/CommandLineOption.ml
+++ b/infer/src/base/CommandLineOption.ml
@@ -362,7 +362,8 @@ let mk_path_helper ~setter ~default_to_string
          that [!arg_being_parsed] points at the option name position in [!args_to_parse], as is the
          case e.g. when calling
          [Arg.parse_argv_dynamic ~current:arg_being_parsed !args_to_parse ...]. *)
-      let abs_path = Utils.filename_to_absolute str in
+      let root = Unix.getcwd () in
+      let abs_path = Utils.filename_to_absolute ~root str in
       (!args_to_parse).(!arg_being_parsed + 1) <- abs_path;
       abs_path
     ) else
diff --git a/infer/src/base/Config.ml b/infer/src/base/Config.ml
index 93284080b..d887eec60 100644
--- a/infer/src/base/Config.ml
+++ b/infer/src/base/Config.ml
@@ -263,8 +263,9 @@ let models_jar =
   lib_dir ^/ "java" ^/ "models.jar"
 
 let models_src_dir =
+  let root = Unix.getcwd () in
   let dir = bin_dir ^/ Filename.parent_dir_name ^/ "models" in
-  Utils.filename_to_absolute dir (* Normalize the path *)
+  Utils.filename_to_absolute ~root dir (* Normalize the path *)
 
 let relative_cpp_extra_include_dir = "cpp" ^/ "include"
 
@@ -304,7 +305,7 @@ let init_work_dir, is_originator =
 
 (** Resolve relative paths passed as command line options, i.e., with respect to the working
     directory of the initial invocation of infer. *)
-let resolve = Utils.filename_to_absolute
+let resolve = Utils.filename_to_absolute ~root:init_work_dir
 
 
 (** Command Line options *)
diff --git a/infer/src/base/Utils.ml b/infer/src/base/Utils.ml
index 6d5d54de8..2e1e62d09 100644
--- a/infer/src/base/Utils.ml
+++ b/infer/src/base/Utils.ml
@@ -105,7 +105,7 @@ let close_outf outf =
 
 
 (** Convert a filename to an absolute one if it is relative, and normalize "." and ".." *)
-let filename_to_absolute fname =
+let filename_to_absolute ~root fname =
   let add_entry rev_done entry =
     match entry, rev_done with
     | ".", [] -> entry :: rev_done                  (* id on . *)
@@ -115,11 +115,11 @@ let filename_to_absolute fname =
     | "..", _ :: rev_done_parent -> rev_done_parent (* path/dir/.. --> path *)
     | _ -> entry :: rev_done
   in
-  let abs_fname = if Filename.is_absolute fname then fname else (Unix.getcwd ()) ^/ fname in
+  let abs_fname = if Filename.is_absolute fname then fname else root ^/ fname in
   Filename.of_parts (List.rev (List.fold_left ~f:add_entry ~init:[] (Filename.parts abs_fname)))
 
 
-(** Convert an absolute filename to one relative to the current directory. *)
+(** Convert an absolute filename to one relative to the given directory. *)
 let filename_to_relative root fname =
   let rec relativize_if_under origin target =
     match origin, target with
diff --git a/infer/src/base/Utils.mli b/infer/src/base/Utils.mli
index 2d13fec94..90c93d002 100644
--- a/infer/src/base/Utils.mli
+++ b/infer/src/base/Utils.mli
@@ -30,7 +30,7 @@ val copy_file : string -> string -> int option
 val read_file : string -> string list option
 
 (** Convert a filename to an absolute one if it is relative, and normalize "." and ".." *)
-val filename_to_absolute : string -> string
+val filename_to_absolute : root:string -> string -> string
 
 (** Convert an absolute filename to one relative to a root directory *)
 val filename_to_relative : string -> string -> string
diff --git a/infer/src/clang/Capture.re b/infer/src/clang/Capture.re
index 31f4ef240..c803cadb6 100644
--- a/infer/src/clang/Capture.re
+++ b/infer/src/clang/Capture.re
@@ -152,9 +152,10 @@ let run_plugin_and_frontend source_path frontend clang_args => {
 
 let cc1_capture clang_cmd => {
   let source_path = {
+    let root = Unix.getcwd ();
     let orig_argv = ClangCommand.get_orig_argv clang_cmd;
     /* the source file is always the last argument of the original -cc1 clang command */
-    Utils.filename_to_absolute orig_argv.(Array.length orig_argv - 1)
+    Utils.filename_to_absolute root::root orig_argv.(Array.length orig_argv - 1)
   };
   Logging.out "@\n*** Beginning capture of file %s ***@\n" source_path;
   if (Config.analyzer == Config.Compile || CLocation.is_file_blacklisted source_path) {
diff --git a/infer/src/java/jClasspath.ml b/infer/src/java/jClasspath.ml
index ab3dc0aca..3e19fdb85 100644
--- a/infer/src/java/jClasspath.ml
+++ b/infer/src/java/jClasspath.ml
@@ -77,7 +77,8 @@ let split_classpath cp = Str.split (Str.regexp JFile.sep) cp
 
 let append_path classpath path =
   if Sys.file_exists path = `Yes then
-    let full_path = Utils.filename_to_absolute path in
+    let root = Unix.getcwd () in
+    let full_path = Utils.filename_to_absolute ~root path in
     if String.length classpath = 0 then
       full_path
     else