Fix rough edges in scaffolded projects (#4)

* fix: remove _workspace hack, keep bare repo properly bare

The project root no longer pretends to be a working directory. The bare
repo stays bare (core.bare=true), HEAD points to main, and git status
correctly reports "this operation must be run in a work tree" at the root.

Removes the orphan _workspace branch, core.bare=false override, and the
root .gitignore wildcard that were only needed to fake a clean status.

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

* fix: wt-add supports existing local and remote branches

Previously always used -b, failing if the branch existed. Now checks
for existing local branches and remote tracking branches before falling
back to creating a new branch from base.

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

* fix: wt-rm deletes local branch and guards against removing main

Now deletes the local branch after removing the worktree. If the branch
has unmerged changes, warns the user and shows the force-delete command
instead of silently dropping work. Refuses to remove the main worktree.

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

* fix: remote-add checks for existing remote and doesn't auto-push

Now errors if the remote name already exists (showing current URL and
how to replace it). No longer pushes main automatically; instead prints
the push command so the user stays in control.

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

* docs: update AGENTS.md for bare repo root behavior

Remove references to _workspace branch and root .gitignore. Document
that the project root is a container (not a working directory) and that
git commands should be run from inside worktrees.

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

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: davidpoblador

template/.mise/tasks/remote-add

@@ -1,17 +1,25 @@
 #!/bin/bash
-#MISE description="Add an existing GitHub repo as a remote and push main"
+#MISE description="Add an existing GitHub repo as a remote and fetch branches"
 
 set -euo pipefail
 
-REPO="${1:?Usage: mise run remote-add <owner/repo>}"
+REPO="${1:?Usage: mise run remote-add <owner/repo> [remote-name]}"
 NAME="${2:-origin}"
 URL="git@github.com:${REPO}.git"
 
+if git remote get-url "$NAME" &>/dev/null; then
+  echo "Error: remote '$NAME' already exists." >&2
+  echo "  Current URL: $(git remote get-url "$NAME")" >&2
+  echo "  To replace it: git remote set-url $NAME $URL" >&2
+  exit 1
+fi
+
 git remote add "$NAME" "$URL"
 git config "remote.$NAME.fetch" "+refs/heads/*:refs/remotes/$NAME/*"
 git fetch "$NAME"
-git push -u "$NAME" main
 
 echo ""
-echo "Remote '$NAME' added and main branch pushed."
+echo "Remote '$NAME' added and branches fetched."
 echo "  $URL"
+echo ""
+echo "To push main: git push -u $NAME main"

template/.mise/tasks/wt-add

@@ -1,11 +1,22 @@
 #!/bin/bash
-#MISE description="Create a new git worktree with a fresh branch"
+#MISE description="Create a new git worktree for a branch"
 
 set -euo pipefail
 
 BRANCH="${1:?Usage: mise run wt-add <branch-name> [base-branch]}"
 BASE="${2:-main}"
 
-git worktree add -b "$BRANCH" "$BRANCH" "$BASE"
-echo "Created worktree '$BRANCH' from '$BASE'"
+if git show-ref --verify --quiet "refs/heads/$BRANCH"; then
+  # Local branch exists, check it out
+  git worktree add "$BRANCH" "$BRANCH"
+  echo "Checked out existing branch '$BRANCH'"
+elif git show-ref --verify --quiet "refs/remotes/origin/$BRANCH"; then
+  # Remote branch exists, track it
+  git worktree add "$BRANCH" "$BRANCH"
+  echo "Checked out '$BRANCH' (tracking origin/$BRANCH)"
+else
+  # New branch, create from base
+  git worktree add -b "$BRANCH" "$BRANCH" "$BASE"
+  echo "Created new branch '$BRANCH' from '$BASE'"
+fi
 echo "  cd $BRANCH/"

template/.mise/tasks/wt-rm

@@ -1,9 +1,20 @@
 #!/bin/bash
-#MISE description="Remove a git worktree and its directory"
+#MISE description="Remove a git worktree and its local branch"
 
 set -euo pipefail
 
 BRANCH="${1:?Usage: mise run wt-rm <branch-name>}"
 
+if [ "$BRANCH" = "main" ]; then
+  echo "Error: refusing to remove the main worktree." >&2
+  exit 1
+fi
+
 git worktree remove "$BRANCH"
-echo "Removed worktree '$BRANCH'"
+
+if ! git branch -d "$BRANCH" 2>/dev/null; then
+  echo "Worktree removed but branch '$BRANCH' has unmerged changes."
+  echo "  To delete it anyway: git branch -D $BRANCH"
+else
+  echo "Removed worktree and branch '$BRANCH'"
+fi

template/AGENTS.md

@@ -30,8 +30,9 @@ This project uses a **bare repo + worktree** structure. Read this before making
    basing new branches, not for edits.
 2. **Each worktree is a full checkout** of a branch. You `cd` into a worktree directory to work on
    that branch. There is no `git checkout` or `git switch` needed.
-3. **Git commands work from the project root**. The `.git` pointer file connects to `.bare/`.
-   The root is on a `_workspace` branch (empty tree) so `git status` returns clean.
+3. **The project root is a container, not a working directory**. The `.git` pointer file connects
+   to `.bare/`. Running `git status` at the root will say "must be run in a work tree", which
+   is correct. Always `cd` into a worktree to do git operations on that branch.
 4. **Files at the project root** (outside worktrees) are not tracked by git. The `.mise/` tasks,
    `AGENTS.md`, and config directories live here intentionally.
 
@@ -67,18 +68,17 @@ If the project was created without a remote URL, use one of these to connect it:
 mise run repo-public owner/repo-name
 mise run repo-private owner/repo-name
 
-# Or add an existing remote
+# Or add an existing remote and fetch branches
 mise run remote-add owner/repo
 ```
 
 ## When running commands
 
-- Always `cd` into the appropriate worktree directory before running build, test, or lint commands.
-- To compare branches, use `git diff main...<branch>` from the project root.
-- To fetch updates: `git fetch --all` from anywhere in the project.
+- Always `cd` into the appropriate worktree directory before running build, test, lint, or git commands.
+- To compare branches from a worktree: `git diff main...<branch>`.
+- To fetch updates: `git fetch --all` from any worktree.
 
 ## Local excludes
 
-The project root has a `.gitignore` containing `*` so all root-level files stay untracked.
-This only affects the `_workspace` checkout; linked worktrees have their own `.gitignore`.
-Use `.bare/info/exclude` only for patterns that should apply across all worktrees.
+Each worktree has its own `.gitignore`. Use `.bare/info/exclude` for patterns that should
+apply across all worktrees.

template/setup.sh.jinja

@@ -26,20 +26,6 @@ else
   git worktree add main main
 fi
 
-# Make git status work at the project root so shell prompts (starship, etc.)
-# don't show spurious indicators. An empty orphan branch means "nothing tracked
-# here" and a wildcard .gitignore hides all untracked project-root files.
-git config core.bare false
-EMPTY_TREE=$(git hash-object -t tree /dev/null)
-EMPTY_COMMIT=$(echo "workspace root" | git commit-tree "$EMPTY_TREE")
-git update-ref refs/heads/_workspace "$EMPTY_COMMIT"
-git symbolic-ref HEAD refs/heads/_workspace
-
-# The project root is on the _workspace branch (empty tree). A wildcard .gitignore
-# here keeps git status clean without polluting .bare/info/exclude, which is
-# shared across all linked worktrees.
-echo "*" > .gitignore
-
 # Create directories for scratchpad and agent config
 mkdir -p _ .claude