Fix legacy bsb to use source subdirectory from output_prefix

The previous implementation used a ninja variable $in_d which doesn't exist,
causing files to be written to the wrong location. Now bsc extracts the
source subdirectory directly from the output_prefix parameter.

For in-source builds with output_prefix='src/Node', files are written to:
  project_root / '.' / 'src' / 'Node.mjs'

For out-of-source builds with output_prefix='src/Node', files go to:
  project_root / 'lib/es6' / 'src' / 'Node.mjs'

This ensures source directory structure is preserved in the output.

Author: nojaf

compiler/bsb/bsb_package_specs.ml

@@ -132,12 +132,14 @@ let from_json suffix (x : Ext_json_types.t) : Spec_set.t =
 
 [@@@warning "+9"]
 
-let package_flag ({format; in_source; suffix} : Bsb_spec_set.spec) dir =
+let package_flag ({format; in_source; suffix} : Bsb_spec_set.spec) _dir =
   (* Generate separate flags for module system, suffix, and output path *)
   let module_system_flag = "-bs-module-system " ^ string_of_format format in
   let suffix_flag = "-bs-suffix " ^ suffix in
+  (* For in-source, use "." as base dir; for out-of-source, use lib/es6 etc.
+     bsc will extract source subdirectory from output_prefix automatically *)
   let output_path =
-    if in_source then dir else Bsb_config.top_prefix_of_format format // dir
+    if in_source then "." else Bsb_config.top_prefix_of_format format
   in
   let output_flag = "-bs-package-output " ^ output_path in
   (* Concatenate all three flags *)

compiler/core/lam_compile_main.ml

@@ -304,9 +304,16 @@ let lambda_as_module
         let basename =  
           Ext_namespace.change_ext_ns_suffix (Filename.basename output_prefix) suffix
         in
+        (* Extract source subdirectory from output_prefix (e.g., "src/acyc" from "src/acyc/Node") *)
+        let source_subdir = Filename.dirname output_prefix in
+        (* Construct target path:
+           - path is the base output directory from config (e.g., "." for in-source, "../lib/es6" for out-of-source)
+           - source_subdir preserves the source directory structure
+           - basename is the final filename *)
         let target_file = 
           (Lazy.force Ext_path.package_dir //
            path //
+           source_subdir //
            basename
            (* #913 only generate little-case js file *)
           ) in