fix(topgrade): make managed config effective, fix disable list

- Merge active settings from shadow ~/.config/topgrade.toml (set_title,
  assume_yes, disable, git repos) into chezmoi-managed file; topgrade
  prefers the former path, so the managed config was never read.
- Replace invalid 'oh-my-zsh' step with 'shell' (no per-framework
  variant) — config failed to deserialize, so no steps were disabled.
- Delete shadow config; topgrade now reads the chezmoi-managed file.

dot_config/topgrade/topgrade.toml

@@ -10,12 +10,28 @@
 # Without this, topgrade will pause for password mid-run on each sudo invocation.
 pre_sudo = true
 
+# Do not set the terminal title.
+set_title = false
+
+# Don't ask for confirmations.
+assume_yes = true
+
+# Disable specific steps — same option names as the CLI flag.
+# `shell` covers the oh-my-zsh step (topgrade has no per-framework variant).
+disable = ["chezmoi", "emacs", "uv", "distrobox", "shell"]
+
 # No ignore_failures — any step failure halts the run; nothing is skipped.
 
 # Print the time in step titles for verbose output.
 display_time = true
 
+[git]
+# Additional git repositories to pull (besides the predefined ones).
+repos = [
+    "~/Documents/Git/*"
+]
+
 [commands]
 # Bump neovim to the version pinned in update-neovim.sh. Idempotent — no-op
 # if already at target. Edit NVIM_TARGET_VERSION in the script to upgrade.
-"~/.local/bin/update-neovim.sh" = "neovim"
+"~/.local/bin/update-neovim.sh" = "neovim"