diff --git a/skills/hf-cli/spec.yaml b/skills/hf-cli/spec.yaml
index 5547c691..7b4a7c6b 100644
--- a/skills/hf-cli/spec.yaml
+++ b/skills/hf-cli/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/hf-cli"
-  version: "0.3.0"
+  version: "0.4.0"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
diff --git a/skills/hf-mcp/spec.yaml b/skills/hf-mcp/spec.yaml
index 09e6f6a7..8361c166 100644
--- a/skills/hf-mcp/spec.yaml
+++ b/skills/hf-mcp/spec.yaml
@@ -11,9 +11,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "hf-mcp/skills/hf-mcp"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
@@ -53,6 +53,8 @@ security:
       reason: "FP: cisco-ai-skill-scanner matched documentation prose/code examples; no executable threat. huggingface/skills @35810a6dbe518a0f7bd99b1e6550cb57b266ff0b."
     - rule_id: LLM_COMMAND_INJECTION
       reason: "Risk accepted by maintainer (ozz@stacklok.com, 2026-06-03): documented first-party HF Hub MCP behavior. SKILL.md shows passing script/shell-command content to the hf_jobs tool, which by design executes user-authored jobs on HF Jobs cloud GPU containers. This execution surface is inherent to the HF MCP server's purpose (running training/compute jobs); it is user-initiated and runs in ephemeral remote containers, not covert injection."
+    - rule_id: LLM_SUPPLY_CHAIN_ATTACK
+      reason: "Risk accepted by maintainer (danbarr, 2026-09-18): the documented training example installs the Hugging Face-maintained transformers and trl packages at runtime in a user-initiated, ephemeral HF Jobs container. Jobs needing private-repository access explicitly receive an HF token, so mutable package dependencies in that environment carry supply-chain exposure; this is accepted as part of the skill's first-party remote-compute workflow."
     - rule_id: LLM_DATA_EXFILTRATION
       reason: "Risk accepted by maintainer (ozz@stacklok.com, 2026-06-03): SKILL.md documents passing HF_TOKEN as a job secret to hf_jobs so remote jobs can authenticate to the HF Hub. Forwarding the user's own HF credential to HF's own job infrastructure is first-party, user-initiated authentication inherent to the HF MCP server; not covert third-party data exfiltration."
     - rule_id: LLM_PROMPT_INJECTION
diff --git a/skills/huggingface-datasets/spec.yaml b/skills/huggingface-datasets/spec.yaml
index a1b9cc09..ccd0d168 100644
--- a/skills/huggingface-datasets/spec.yaml
+++ b/skills/huggingface-datasets/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/huggingface-datasets"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
diff --git a/skills/huggingface-gradio/spec.yaml b/skills/huggingface-gradio/spec.yaml
index 0362d39d..e9ae66a0 100644
--- a/skills/huggingface-gradio/spec.yaml
+++ b/skills/huggingface-gradio/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/huggingface-gradio"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
diff --git a/skills/huggingface-paper-publisher/spec.yaml b/skills/huggingface-paper-publisher/spec.yaml
index 306470da..4e71b576 100644
--- a/skills/huggingface-paper-publisher/spec.yaml
+++ b/skills/huggingface-paper-publisher/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/huggingface-paper-publisher"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
diff --git a/skills/huggingface-tool-builder/spec.yaml b/skills/huggingface-tool-builder/spec.yaml
index d83d4cee..65fba8e9 100644
--- a/skills/huggingface-tool-builder/spec.yaml
+++ b/skills/huggingface-tool-builder/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/huggingface-tool-builder"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
diff --git a/skills/huggingface-trackio/spec.yaml b/skills/huggingface-trackio/spec.yaml
index 2bdeadef..5d4caab9 100644
--- a/skills/huggingface-trackio/spec.yaml
+++ b/skills/huggingface-trackio/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/huggingface-trackio"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"
diff --git a/skills/transformers-js/spec.yaml b/skills/transformers-js/spec.yaml
index fc395d37..e695e1df 100644
--- a/skills/transformers-js/spec.yaml
+++ b/skills/transformers-js/spec.yaml
@@ -9,9 +9,9 @@ metadata:
 
 spec:
   repository: "https://github.com/huggingface/skills"
-  ref: "ec0108293521ef698e451ec044e8b4feba6b732b"  # main as of 2026-04-16
+  ref: "abc20ae526d8b4c0e4dff89f904adce28a4a0eb6"  # main as of 2026-04-16
   path: "skills/transformers-js"
-  version: "0.3.0"
+  version: "0.3.1"
 
 provenance:
   repository_uri: "https://github.com/huggingface/skills"