chore: General cleanup and minor configuration adjustments

.gitignore

@@ -1,4 +1,10 @@
 # VS Code — only shared workspace settings
 .vscode/*
+!.vscode/
 !.vscode/settings.json
 !.vscode/extensions.json
+
+# framework
+/master-knowledge-genome/
+/keys/
+*.key

globals.env

@@ -9,7 +9,7 @@ PROVIDER=forgejo
 
 # --- FORGEJO ---
 FORGEJO_URL=https://git.keruhomelab.com
-FORGEJO_USER=keru
+FORGEJO_USER=Keru
 FORGEJO_SSH_PORT=222
 
 # --- GITHUB (used when PROVIDER=github) ---

skills/ingest/scripts/index-append.py

@@ -4,11 +4,6 @@
 # Insert an entry line into the correct section of wiki/index.md and keep that
 # section's entries alphabetically ordered. Bumps frontmatter last_updated.
 #
-# NOTE: agents-genome.md and wiki-index.md claim the pre-commit hook sorts the
-# index. The actual pre-commit.sh only runs the plaintext-leak check — it does
-# NOT sort. This script owns the ordering instead. (If you later move sorting
-# into the hook, reduce this to a plain append.)
-#
 #   index-append.py --section Sources \
 #       --entry '- [[sources/foo]] — One-line summary. `maturity: draft`'
 # =============================================================================

templates/wiki-log.md

@@ -57,7 +57,7 @@ grep "^## \[2026-05" wiki/log.md
 ## [{{DATE}}] CONFIG | Genome scaffolded
 
 - run_id: `system-init`
-- model: `setup-knowledge-genome.sh`
+- model: `scaffold.sh`
 - context_read: _(none — initial scaffold)_
 - output_written: `[[wiki/index.md]]`, `[[wiki/log.md]]`, `[[AGENTS.md]]`
 - reasoning: Initial directory structure and encryption layer initialized by setup script.