refactor: isolate custom flake inputs to minimize upstream divergence

Implements best-practice pattern for managing custom package sources:
- Main nixpkgs now uses upstream NixOS/nixpkgs/nixos-unstable
- nixpkgs-docling isolated for ONLY docling-parse fix (temporary until PR #184 merges)
- home-manager-wsl isolated for WSL hosts (windows-terminal feature WIP)
- Upstream home-manager for non-WSL hosts (mbp, potato, nixvim-minimal)

Benefits:
- 99% of packages now from upstream (easier debugging, faster updates)
- Custom fixes isolated to specific packages via overlays
- Clear migration path when upstream PRs merge
- Reduced system closure duplication

Technical changes:
- flake.nix: Split nixpkgs into upstream + nixpkgs-docling
- overlays/default.nix: Import nixpkgs-docling only for docling package
- flake-modules/overlays.nix: Pass inputs to overlay function
- flake-modules/home-configurations.nix: WSL hosts use home-manager-wsl

Note: Using local path for home-manager-wsl until branch is pushed to GitHub

Related to docling-parse PR: docling-project/docling-parse#184

Author: timblaktu

flake-modules/home-configurations.nix

@@ -38,7 +38,7 @@
       );
 
       "tim@thinky-ubuntu" = withSystem "x86_64-linux" ({ pkgs, ... }:
-        inputs.home-manager.lib.homeManagerConfiguration {
+        inputs.home-manager-wsl.lib.homeManagerConfiguration {
           inherit pkgs;
           modules = [
             { nixpkgs.config.allowUnfree = true; }
@@ -78,7 +78,7 @@
       );
 
       "tim@pa161878-nixos" = withSystem "x86_64-linux" ({ pkgs, ... }:
-        inputs.home-manager.lib.homeManagerConfiguration {
+        inputs.home-manager-wsl.lib.homeManagerConfiguration {
           inherit pkgs;
           modules = [
             { nixpkgs.config.allowUnfree = true; }
@@ -169,7 +169,7 @@
       );
 
       "tim@thinky-nixos" = withSystem "x86_64-linux" ({ pkgs, ... }:
-        inputs.home-manager.lib.homeManagerConfiguration {
+        inputs.home-manager-wsl.lib.homeManagerConfiguration {
           inherit pkgs;
           modules = [
             { nixpkgs.config.allowUnfree = true; }

flake-modules/overlays.nix

@@ -9,7 +9,7 @@
   flake = {
     # Export overlays for other flakes to use
     overlays = {
-      default = import ../overlays;
+      default = import ../overlays { inherit inputs; };
     };
   };
 }

flake.nix

@@ -2,11 +2,16 @@
   description = "Unified Nix configuration for all systems";
 
   inputs = {
-    # nixpkgs.url = "github:timblaktu/nixpkgs/writers-auto-detection";
-    nixpkgs.url = "github:timblaktu/nixpkgs/docling-parse-fix"; # Includes docling-parse PR #184 fix
-    # nixpkgs.url = "git+file:///home/tim/src/nixpkgs?ref=docling-parse-fix&shallow=true";  # For local dev
+    # MAIN NIXPKGS - upstream, used for 99% of packages
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
     nixpkgs-stable.url = "github:NixOS/nixpkgs/nixos-24.11";
-    # nixpkgs-unstable for nixvim (has postgres-lsp and other recent packages)
+
+    # CUSTOM NIXPKGS - isolated inputs for packages needing specific fixes
+    # Temporary: Only for docling-parse until PR #184 merges upstream
+    nixpkgs-docling.url = "github:timblaktu/nixpkgs/docling-parse-fix";
+    # nixpkgs-docling.url = "git+file:///home/tim/src/nixpkgs?ref=docling-parse-fix&shallow=true";  # For local dev
+
+    # For nixvim (needs postgres-lsp and other recent packages)
     nixpkgs-unstable.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
 
     # flake-parts for modular flake organization
@@ -19,18 +24,20 @@
       inputs.nixpkgs.follows = "nixpkgs-unstable";
     };
 
-    home-manager = {
-      # url = "github:timblaktu/home-manager/wsl-windows-terminal";
-      url = "git+file:///home/tim/src/home-manager?ref=wsl-windows-terminal";
-      inputs.nixpkgs.follows = "nixpkgs";
-    };
+    # HOME-MANAGER - upstream for non-WSL hosts
+    home-manager.url = "github:nix-community/home-manager";
+    home-manager.inputs.nixpkgs.follows = "nixpkgs";
 
-    nixos-wsl = {
-      url = "github:timblaktu/NixOS-WSL/plugin-shim-integration";
-      # url = "github:timblaktu/NixOS-WSL/feature/bare-mount-support";
-      # url = "git+file:///home/tim/src/NixOS-WSL";
-      inputs.nixpkgs.follows = "nixpkgs";
-    };
+    # HOME-MANAGER CUSTOM - WSL-specific fork for windows-terminal feature (WIP)
+    # home-manager-wsl.url = "github:timblaktu/home-manager/wsl-windows-terminal";  # Use after pushing branch
+    home-manager-wsl.url = "git+file:///home/tim/src/home-manager?ref=wsl-windows-terminal";  # For local dev
+    home-manager-wsl.inputs.nixpkgs.follows = "nixpkgs";
+
+    # NIXOS-WSL - custom fork for plugin-shim-integration (WIP)
+    nixos-wsl.url = "github:timblaktu/NixOS-WSL/plugin-shim-integration";
+    # nixos-wsl.url = "github:timblaktu/NixOS-WSL/feature/bare-mount-support";
+    # nixos-wsl.url = "git+file:///home/tim/src/NixOS-WSL";  # For local dev
+    nixos-wsl.inputs.nixpkgs.follows = "nixpkgs";
 
     darwin = {
       url = "github:lnl7/nix-darwin";
@@ -50,7 +57,6 @@
       inputs.nixpkgs.follows = "nixpkgs";
     };
 
-
     nix-writers.url = "github:timblaktu/nix-writers";
   };
 
@@ -76,12 +82,12 @@
 
       # Per-system configuration
       perSystem = { config, self', inputs', pkgs, system, ... }: {
-        # Configure nixpkgs for this system
+        # Configure nixpkgs for this system (now uses upstream nixpkgs)
         _module.args.pkgs = import inputs.nixpkgs {
           inherit system;
           config.allowUnfree = true;
           overlays = [
-            (import ./overlays)
+            (import ./overlays { inherit inputs; })
           ];
         };
       };

overlays/default.nix

@@ -1,13 +1,24 @@
 # Overlays for the Nix configuration
+{ inputs }:
 final: prev:
 let
   customPkgs = import ../pkgs { pkgs = prev; };
+
+  # Import nixpkgs-docling ONLY for docling-parse fix (isolated)
+  # This ensures only docling packages use the custom fork
+  pkgsDocling = import inputs.nixpkgs-docling {
+    inherit (prev) system;
+    config.allowUnfree = true;
+  };
 in
 {
   # Custom packages and overrides go here
   markitdown = customPkgs.markitdown;
   marker-pdf = customPkgs.marker-pdf;
 
+  # ISOLATED: docling from custom nixpkgs (temporary until PR #184 merges)
+  docling = pkgsDocling.docling;
+
   # Fix watchfiles test failure that affects MCP servers
   # Fallback: Disable problematic tests while working on version update
   pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [