Exclude dotfiles by default, add --include-dotfiles flag

Changed the default behavior to exclude dotfiles (files/dirs starting with .)
which is the more common use case. Added --include-dotfiles flag for when
hidden files need to be included in the manifest.

README.md

@@ -101,7 +101,7 @@ Reading file contents and computing cryptographic hashes for manifest generation
 ### scanner.go
 - **Types**
   - `Options struct` - Options for scanner behavior
-    - `IgnoreDotfiles bool`
+    - `IncludeDotfiles bool` - Include dot (hidden) files (excluded by default)
     - `FollowSymLinks bool`
   - `EnumerateStatus struct` - Progress information for enumeration phase
     - `FilesFound int64`
@@ -171,7 +171,7 @@ Reading file contents and computing cryptographic hashes for manifest generation
 ### manifest.go
 - **Types**
   - `ManifestScanOptions struct` - Options for scanning directories
-    - `IgnoreDotfiles bool`
+    - `IncludeDotfiles bool` - Include dot (hidden) files (excluded by default)
     - `FollowSymLinks bool`
 - **Functions**
   - `New() *manifest` - Creates a new empty manifest