Flatten document skills so all 26 are discoverable (v2.21.0)

The docx, pdf, pptx, and xlsx skills lived at skills/document-skills/<name>/,
one level deeper than any client scans. Agent Plugins section 7.1 states that
"Clients MUST NOT recursively search deeper descendants for additional
skills", so all four were invisible to every Agent Plugins client and to
Claude Code.

The nesting came from this repository, not upstream: skills.lock.json
rewrote each skill's path through its "destination" field.
scientific-agent-skills publishes all four as top-level skills and has no
document-skills directory. Re-vendoring the same pinned commit with flat
destinations fixes it here; snapshot_sha256 was regenerated and the
per-skill hashes are unchanged, so provenance holds.

- skills.lock.json: destinations are now single path segments
- .claude-plugin/marketplace.json: registers each of the four individually
- check_consistency.py: drops the SKILL_BUNDLE_DIRS escape hatch, which
  existed only to let the bundle pass frontmatter checks while its
  sub-skills stayed undiscoverable

validate_agent_plugin.py now reports 26 skills and zero warnings across all
three plugin roots.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Author: TKassis

.claude-plugin/marketplace.json

@@ -2,7 +2,7 @@
   "name": "claude-scientific-writer",
   "metadata": {
     "description": "Skills and setup for scientific writing (papers, grants, posters, clinical reports) using the scientific-writer toolkit.",
-    "version": "2.20.0",
+    "version": "2.21.0",
     "homepage": "https://github.com/K-Dense-AI/claude-scientific-writer"
   },
   "owner": {
@@ -19,7 +19,7 @@
         "./skills/citation-management",
         "./skills/clinical-decision-support",
         "./skills/clinical-reports",
-        "./skills/document-skills",
+        "./skills/docx",
         "./skills/generate-image",
         "./skills/hypothesis-generation",
         "./skills/infographics",
@@ -28,7 +28,9 @@
         "./skills/market-research-reports",
         "./skills/markitdown",
         "./skills/parallel-web",
+        "./skills/pdf",
         "./skills/peer-review",
+        "./skills/pptx",
         "./skills/pptx-posters",
         "./skills/research-grants",
         "./skills/research-lookup",
@@ -38,7 +40,8 @@
         "./skills/scientific-slides",
         "./skills/scientific-writing",
         "./skills/treatment-plans",
-        "./skills/venue-templates"
+        "./skills/venue-templates",
+        "./skills/xlsx"
       ]
     }
   ]

.claude/plugin.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
   "name": "claude-scientific-writer",
-  "version": "2.20.0",
+  "version": "2.21.0",
   "description": "Deep research and scientific writing skills: publication-ready papers, literature reviews, grant proposals, posters, slides, and clinical reports backed by verified citations.",
   "author": {
     "name": "K-Dense Inc.",

.claude/skills.lock.json

@@ -3,7 +3,7 @@
   "repository": "https://github.com/K-Dense-AI/scientific-agent-skills",
   "ref": "ab2f84ab10597c59fac186ecda6d5edd5dcc8b92",
   "commit": "ab2f84ab10597c59fac186ecda6d5edd5dcc8b92",
-  "snapshot_sha256": "01d64156c9acf8acb0bce8a9a527907a579afcc4306d456da19a91aae852cf2a",
+  "snapshot_sha256": "b5a3d19457452148db098bab0620fdefd34302d1d26a8e96c0e90c8204d10bce",
   "skills": [
     {
       "source": "citation-management",
@@ -22,22 +22,22 @@
     },
     {
       "source": "docx",
-      "destination": "document-skills/docx",
+      "destination": "docx",
       "sha256": "297eabe17185286e63696c5e99cc263838e00cffb9ad5e44add9b0455487307f"
     },
     {
       "source": "pdf",
-      "destination": "document-skills/pdf",
+      "destination": "pdf",
       "sha256": "a168863ca17d8d82b10ca343f6d07d91765a14f2a61d7d6ddb6d248dc48aebe9"
     },
     {
       "source": "pptx",
-      "destination": "document-skills/pptx",
+      "destination": "pptx",
       "sha256": "bdb280197d933df17f4436a3f34be5aa06e1b4e6cf52d73d74b62157c5915915"
     },
     {
       "source": "xlsx",
-      "destination": "document-skills/xlsx",
+      "destination": "xlsx",
       "sha256": "dbb2a5ae521c3e16c0864329bdfd5c8491d7e2e52295bfaefe432b570d67e882"
     },
     {