fix: resolve issue #299 and Phase 1 cleanup

- Fix #299: rename --chunk-size/--chunk-overlap to --streaming-chunk-size/
  --streaming-overlap in arguments/package.py to avoid collision with the
  RAG --chunk-size flag from arguments/common.py
- Phase 1a: make package_skill.py import args via add_package_arguments()
  instead of a 105-line inline duplicate argparse block; fixes the root
  cause of _reconstruct_argv() passing unrecognised flag names
- Phase 1b: centralise setup_logging() into utils.py and remove 4
  duplicate module-level logging.basicConfig() calls from doc_scraper.py,
  github_scraper.py, codebase_scraper.py, and unified_scraper.py
- Fix test_package_structure.py / test_cli_paths.py version strings
  (3.1.1 → 3.1.2)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/skill_seekers/cli/arguments/package.py

@@ -70,8 +70,8 @@ PACKAGE_ARGUMENTS: dict[str, dict[str, Any]] = {
             "help": "Use streaming ingestion for large docs (memory-efficient)",
         },
     },
-    "chunk_size": {
-        "flags": ("--chunk-size",),
+    "streaming_chunk_size": {
+        "flags": ("--streaming-chunk-size",),
         "kwargs": {
             "type": int,
             "default": 4000,
@@ -79,12 +79,12 @@ PACKAGE_ARGUMENTS: dict[str, dict[str, Any]] = {
             "metavar": "N",
         },
     },
-    "chunk_overlap": {
-        "flags": ("--chunk-overlap",),
+    "streaming_overlap": {
+        "flags": ("--streaming-overlap",),
         "kwargs": {
             "type": int,
             "default": 200,
-            "help": "Overlap between chunks (streaming mode, default: 200)",
+            "help": "Character overlap between chunks (streaming mode, default: 200)",
             "metavar": "N",
         },
     },