[GHA] Fix samples dependabot duplicated PRs (#3031)

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## Description
Duplicated PR:
#3014
#3015
There is some inconsistency how `/samples` and `/tests` scanned. This is
a fix attempt. Group directories and prefix samples with `.`

Author: as-suvorov

.github/dependabot.yml

@@ -12,7 +12,7 @@ updates:
       time: "09:00"
       timezone: "Europe/Dublin"
     open-pull-requests-limit: 3
-    
+
   #
   # Enable version updates for npm
   #
@@ -24,44 +24,17 @@ updates:
       timezone: "Europe/Dublin"
     open-pull-requests-limit: 3
     versioning-strategy: increase-if-necessary
-    
+
   #
   # Python dependencies
   #
   - package-ecosystem: "pip"
-    directory: "./tests/python_tests/"
-    schedule:
-      interval: "daily"
-      time: "09:00"
-      timezone: "Europe/Dublin"
-    versioning-strategy: increase-if-necessary
-      
-  - package-ecosystem: "pip"
-    directory: "./tools/llm_bench/"
-    schedule:
-      interval: "daily"
-      time: "09:00"
-      timezone: "Europe/Dublin"
-    versioning-strategy: increase-if-necessary
-      
-  - package-ecosystem: "pip"
-    directory: "./tools/who_what_benchmark/"
-    schedule:
-      interval: "daily"
-      time: "09:00"
-      timezone: "Europe/Dublin"
-    versioning-strategy: increase-if-necessary
-      
-  - package-ecosystem: "pip"
-    directory: "samples/"
-    schedule:
-      interval: "daily"
-      time: "09:00"
-      timezone: "Europe/Dublin"
-    versioning-strategy: increase-if-necessary
-      
-  - package-ecosystem: "pip"
-    directory: "/"
+    directories:
+      - "/"
+      - "./samples/"
+      - "./tests/python_tests/"
+      - "./tools/llm_bench/"
+      - "./tools/who_what_benchmark/"
     schedule:
       interval: "daily"
       time: "09:00"