fix: update worktree .git pointers after forward repo migration

bin/wt-context

@@ -175,32 +175,13 @@ remove_context() {
     git -C "$repo_root" config --local --remove-section wt 2>/dev/null || true
   fi
 
-  # 2. Remove adoption markers from worktrees
-  info "Removing adoption markers from worktrees..."
-  wt_source wt-adopt
-  local wt_path=""
-  while IFS= read -r line; do
-    if [[ "$line" == "worktree "* ]]; then
-      wt_path="${line#worktree }"
-    elif [[ -z "$line" && -n "$wt_path" ]]; then
-      # End of worktree block — check and remove marker
-      if wt_is_adopted "$wt_path" 2>/dev/null; then
-        local marker_ctx
-        marker_ctx="$(wt_read_adopted_context "$wt_path" 2>/dev/null)" || true
-        # Remove if context matches, or if it's an old empty marker
-        if [[ -z "$marker_ctx" || "$marker_ctx" == "$context_name" ]]; then
-          wt_unmark_adopted "$wt_path" 2>/dev/null || true
-        fi
-      fi
-      wt_path=""
-    fi
-  done < <(git -C "$repo_root" worktree list --porcelain 2>/dev/null; echo)
-
-  # 3. Delete .conf file
+  # 2. Delete .conf file
   info "Removing config file..."
   rm -f "$conf_file"
 
-  # 4. Reverse repo migration: move main repo back to symlink location
+  # 3. Reverse repo migration: move main repo back to symlink location
+  # Done BEFORE removing adoption markers so pointer update can check adoption state
+  wt_source wt-adopt
   if [[ -L "$active_worktree" ]]; then
     local link_target
     link_target="$(readlink "$active_worktree")"
@@ -215,28 +196,11 @@ remove_context() {
       mv "$repo_root" "$active_worktree"
 
       # Fix worktree .git pointers after repo move
-      # Each worktree has a .git FILE containing "gitdir: <old>/.git/worktrees/<name>"
-      # After moving the repo, these need to point to the new location
-      if [[ -d "$active_worktree/.git/worktrees" ]]; then
-        info "Updating worktree references..."
-        local new_git_dir="$active_worktree/.git"
-
-        for wt_meta_dir in "$new_git_dir"/worktrees/*/; do
-          [[ -d "$wt_meta_dir" ]] || continue
-          # Read the gitdir file to find the worktree's .git file location
-          local gitdir_file="$wt_meta_dir/gitdir"
-          [[ -f "$gitdir_file" ]] || continue
-          local wt_dot_git
-          wt_dot_git="$(cat "$gitdir_file" | tr -d '[:space:]')"
-
-          # Update the .git file in the worktree to point to the new location
-          if [[ -f "$wt_dot_git" ]]; then
-            local wt_name
-            wt_name="$(basename "$wt_meta_dir")"
-            echo "gitdir: ${new_git_dir}/worktrees/${wt_name}" > "$wt_dot_git"
-          fi
-        done
-      fi
+      # Only update worktrees that were adopted by this context
+      _wt_update_worktree_pointers "$active_worktree" "adopted" "$context_name"
+
+      # Update repo_root for subsequent marker removal
+      repo_root="$active_worktree"
     else
       warn "Symlink at $active_worktree points to $link_target (expected $repo_root)"
       warn "Removing symlink but not moving repository"
@@ -246,6 +210,26 @@ remove_context() {
     warn "$active_worktree exists but is not a symlink — leaving it unchanged"
   fi
 
+  # 4. Remove adoption markers from worktrees (after repo migration so pointers are updated first)
+  info "Removing adoption markers from worktrees..."
+  local wt_path=""
+  while IFS= read -r line; do
+    if [[ "$line" == "worktree "* ]]; then
+      wt_path="${line#worktree }"
+    elif [[ -z "$line" && -n "$wt_path" ]]; then
+      # End of worktree block — check and remove marker
+      if wt_is_adopted "$wt_path" 2>/dev/null; then
+        local marker_ctx
+        marker_ctx="$(wt_read_adopted_context "$wt_path" 2>/dev/null)" || true
+        # Remove if context matches, or if it's an old empty marker
+        if [[ -z "$marker_ctx" || "$marker_ctx" == "$context_name" ]]; then
+          wt_unmark_adopted "$wt_path" 2>/dev/null || true
+        fi
+      fi
+      wt_path=""
+    fi
+  done < <(git -C "$repo_root" worktree list --porcelain 2>/dev/null; echo)
+
   # 5. Update ~/.wt/current
   local current_context
   current_context="$(wt_get_current_context)"

lib/wt-common

@@ -297,6 +297,81 @@ wt_read_config || true
 # Context name (for display purposes)
 : "${WT_CONTEXT_NAME:=""}"
 
+# ─────────────────────────────────────────────────────────────────────────────
+# Worktree pointer maintenance
+# ─────────────────────────────────────────────────────────────────────────────
+
+# After moving a repo's .git directory to a new location, update
+# worktrees' .git files to point to the new .git path.
+#
+# Each git worktree has a .git FILE (not directory) containing:
+#   gitdir: /old/path/.git/worktrees/<name>
+#
+# After the repo is moved, these pointers become stale. This function
+# reads the main repo's .git/worktrees/*/gitdir to find each worktree's
+# .git file, then rewrites it to point to the new location.
+#
+# Args: $1 = repo directory (the new location containing .git/)
+#       $2 = mode (optional): "unadopted" (default) - only unadopted worktrees
+#                              "adopted"  - only worktrees adopted by context
+#                              "all"      - all worktrees unconditionally
+#       $3 = context name (optional, used with "adopted" mode)
+_wt_update_worktree_pointers() {
+  local repo_dir="$1"
+  local mode="${2:-unadopted}"
+  local context_name="${3:-}"
+  local git_dir="$repo_dir/.git"
+
+  [[ -d "$git_dir/worktrees" ]] || return 0
+
+  info "Updating worktree references..."
+  for wt_meta_dir in "$git_dir"/worktrees/*/; do
+    [[ -d "$wt_meta_dir" ]] || continue
+
+    # Read gitdir to find the worktree path
+    local gitdir_file="$wt_meta_dir/gitdir"
+    [[ -f "$gitdir_file" ]] || continue
+    local wt_dot_git
+    wt_dot_git="$(cat "$gitdir_file" | tr -d '[:space:]')"
+    [[ -f "$wt_dot_git" ]] || continue
+
+    # Check adoption state based on mode.
+    # We check the marker directly in the worktree metadata dir rather than
+    # using wt_is_adopted (which runs git rev-parse) because after a repo
+    # move the .git pointers are stale and git operations would fail.
+    # The marker lives at <git_dir>/worktrees/<name>/wt/adopted.
+    local adopted_marker="$wt_meta_dir/wt/adopted"
+    case "$mode" in
+      unadopted)
+        # Skip adopted worktrees — they already have correct physical paths
+        if [[ -f "$adopted_marker" ]]; then
+          continue
+        fi
+        ;;
+      adopted)
+        # Skip unadopted worktrees and worktrees adopted by other contexts
+        if [[ ! -f "$adopted_marker" ]]; then
+          continue
+        fi
+        if [[ -n "$context_name" ]]; then
+          local adopted_ctx
+          adopted_ctx="$(head -1 "$adopted_marker" 2>/dev/null | tr -d '[:space:]')"
+          if [[ -n "$adopted_ctx" && "$adopted_ctx" != "$context_name" ]]; then
+            continue
+          fi
+        fi
+        ;;
+      all)
+        # Update everything
+        ;;
+    esac
+
+    local wt_name="${wt_meta_dir%/}"
+    wt_name="${wt_name##*/}"
+    echo "gitdir: ${git_dir}/worktrees/${wt_name}" > "$wt_dot_git"
+  done
+}
+
 # ─────────────────────────────────────────────────────────────────────────────
 # Expand ~ to $HOME in a path (bash doesn't expand ~ in variable assignments
 # or interactive read input)

lib/wt-context-setup

@@ -372,6 +372,12 @@ _wt_migrate_repo() {
     echo "Creating symlink $WT_ACTIVE_WORKTREE -> $WT_MAIN_REPO_ROOT ..."
     ln -s "$WT_MAIN_REPO_ROOT" "$WT_ACTIVE_WORKTREE"
 
+    # Update pre-existing worktree .git pointers to use the physical base path.
+    # Before migration, worktrees pointed to the original location (now the symlink).
+    # After wt switch, the symlink moves away from base, breaking those pointers.
+    # Only update unadopted worktrees — adopted ones already have correct physical paths.
+    _wt_update_worktree_pointers "$WT_MAIN_REPO_ROOT" "unadopted"
+
     echo "  ✓ Migration complete!"
 
   elif [[ -L "$WT_ACTIVE_WORKTREE" ]]; then

test/integration/wt-context-remove.bats

@@ -205,6 +205,11 @@ teardown() {
     # Normalize worktree path
     wt_path="$(cd "$wt_path" && pwd -P)"
 
+    # Mark the worktree as adopted by this context — remove only updates
+    # worktrees adopted by the context being removed
+    source "$TEST_HOME/.wt/lib/wt-adopt"
+    WT_CONTEXT_NAME="ptr-test" wt_mark_adopted "$wt_path"
+
     # Verify the worktree's .git file points to the OLD location
     local dot_git_content
     dot_git_content="$(cat "$wt_path/.git")"

test/unit/wt-context-setup.bats

@@ -8,6 +8,7 @@ setup() {
 
     # Source the libraries under test
     source "$TEST_HOME/.wt/lib/wt-common"
+    source "$TEST_HOME/.wt/lib/wt-adopt"
     source "$TEST_HOME/.wt/lib/wt-context"
     source "$TEST_HOME/.wt/lib/wt-context-setup"
 }
@@ -229,3 +230,186 @@ teardown() {
     assert_success
 }
 
+# =============================================================================
+# Tests for _wt_update_worktree_pointers()
+# =============================================================================
+
+@test "_wt_update_worktree_pointers updates .git files after repo move" {
+    # Create a repo with a worktree
+    local repo
+    repo=$(create_mock_repo "$BATS_TEST_TMPDIR/original-repo")
+    create_branch "$repo" "feat-branch"
+    local wt_path="$BATS_TEST_TMPDIR/wt-feat"
+    create_worktree "$repo" "$wt_path" "feat-branch"
+    wt_path="$(cd "$wt_path" && pwd -P)"
+
+    # Verify initial .git pointer uses old path
+    local dot_git_content
+    dot_git_content="$(cat "$wt_path/.git")"
+    assert_equal "$dot_git_content" "gitdir: ${repo}/.git/worktrees/wt-feat"
+
+    # Simulate migration: move repo to new location
+    local new_repo="$BATS_TEST_TMPDIR/new-location"
+    mv "$repo" "$new_repo"
+
+    # Run the pointer update
+    run _wt_update_worktree_pointers "$new_repo"
+    assert_success
+
+    # .git file should now point to the new location
+    dot_git_content="$(cat "$wt_path/.git")"
+    assert_equal "$dot_git_content" "gitdir: ${new_repo}/.git/worktrees/wt-feat"
+
+    # Verify git operations work
+    run git -C "$wt_path" status
+    assert_success
+}
+
+@test "_wt_update_worktree_pointers is no-op without worktrees" {
+    local repo
+    repo=$(create_mock_repo "$BATS_TEST_TMPDIR/no-wt-repo")
+
+    # Should succeed silently when there are no worktrees
+    run _wt_update_worktree_pointers "$repo"
+    assert_success
+}
+
+@test "_wt_update_worktree_pointers handles multiple worktrees" {
+    local repo
+    repo=$(create_mock_repo "$BATS_TEST_TMPDIR/multi-wt-repo")
+
+    create_branch "$repo" "branch-a"
+    create_branch "$repo" "branch-b"
+    local wt_a="$BATS_TEST_TMPDIR/wt-a"
+    local wt_b="$BATS_TEST_TMPDIR/wt-b"
+    create_worktree "$repo" "$wt_a" "branch-a"
+    create_worktree "$repo" "$wt_b" "branch-b"
+    wt_a="$(cd "$wt_a" && pwd -P)"
+    wt_b="$(cd "$wt_b" && pwd -P)"
+
+    # Move repo
+    local new_repo="$BATS_TEST_TMPDIR/moved-multi"
+    mv "$repo" "$new_repo"
+
+    run _wt_update_worktree_pointers "$new_repo"
+    assert_success
+
+    # Both worktrees should be updated
+    local content_a content_b
+    content_a="$(cat "$wt_a/.git")"
+    content_b="$(cat "$wt_b/.git")"
+    assert_equal "$content_a" "gitdir: ${new_repo}/.git/worktrees/wt-a"
+    assert_equal "$content_b" "gitdir: ${new_repo}/.git/worktrees/wt-b"
+}
+
+@test "_wt_update_worktree_pointers unadopted mode skips adopted worktrees" {
+    local repo
+    repo=$(create_mock_repo "$BATS_TEST_TMPDIR/adopt-skip-repo")
+
+    create_branch "$repo" "branch-adopted"
+    create_branch "$repo" "branch-unadopted"
+    local wt_adopted="$BATS_TEST_TMPDIR/wt-adopted"
+    local wt_unadopted="$BATS_TEST_TMPDIR/wt-unadopted"
+    create_worktree "$repo" "$wt_adopted" "branch-adopted"
+    create_worktree "$repo" "$wt_unadopted" "branch-unadopted"
+    wt_adopted="$(cd "$wt_adopted" && pwd -P)"
+    wt_unadopted="$(cd "$wt_unadopted" && pwd -P)"
+
+    # Mark one worktree as adopted
+    wt_mark_adopted "$wt_adopted"
+
+    # Move repo
+    local new_repo="$BATS_TEST_TMPDIR/moved-adopt-skip"
+    mv "$repo" "$new_repo"
+
+    run _wt_update_worktree_pointers "$new_repo" "unadopted"
+    assert_success
+
+    # Unadopted worktree should be updated
+    local content_unadopted
+    content_unadopted="$(cat "$wt_unadopted/.git")"
+    assert_equal "$content_unadopted" "gitdir: ${new_repo}/.git/worktrees/wt-unadopted"
+
+    # Adopted worktree should NOT be updated (still has old path)
+    local content_adopted
+    content_adopted="$(cat "$wt_adopted/.git")"
+    assert_equal "$content_adopted" "gitdir: ${repo}/.git/worktrees/wt-adopted"
+}
+
+@test "_wt_update_worktree_pointers adopted mode only updates worktrees adopted by context" {
+    local repo
+    repo=$(create_mock_repo "$BATS_TEST_TMPDIR/adopt-ctx-repo")
+
+    create_branch "$repo" "branch-ctx-a"
+    create_branch "$repo" "branch-ctx-b"
+    create_branch "$repo" "branch-unadopted"
+    local wt_ctx_a="$BATS_TEST_TMPDIR/wt-ctx-a"
+    local wt_ctx_b="$BATS_TEST_TMPDIR/wt-ctx-b"
+    local wt_unadopted="$BATS_TEST_TMPDIR/wt-ctx-unadopted"
+    create_worktree "$repo" "$wt_ctx_a" "branch-ctx-a"
+    create_worktree "$repo" "$wt_ctx_b" "branch-ctx-b"
+    create_worktree "$repo" "$wt_unadopted" "branch-unadopted"
+    wt_ctx_a="$(cd "$wt_ctx_a" && pwd -P)"
+    wt_ctx_b="$(cd "$wt_ctx_b" && pwd -P)"
+    wt_unadopted="$(cd "$wt_unadopted" && pwd -P)"
+
+    # Mark worktrees as adopted by different contexts
+    export WT_CONTEXT_NAME="ctx-a"
+    wt_mark_adopted "$wt_ctx_a"
+    export WT_CONTEXT_NAME="ctx-b"
+    wt_mark_adopted "$wt_ctx_b"
+    unset WT_CONTEXT_NAME
+
+    # Move repo
+    local new_repo="$BATS_TEST_TMPDIR/moved-adopt-ctx"
+    mv "$repo" "$new_repo"
+
+    run _wt_update_worktree_pointers "$new_repo" "adopted" "ctx-a"
+    assert_success
+
+    # Only the worktree adopted by ctx-a should be updated
+    local content_a
+    content_a="$(cat "$wt_ctx_a/.git")"
+    assert_equal "$content_a" "gitdir: ${new_repo}/.git/worktrees/wt-ctx-a"
+
+    # Worktree adopted by ctx-b should NOT be updated
+    local content_b
+    content_b="$(cat "$wt_ctx_b/.git")"
+    assert_equal "$content_b" "gitdir: ${repo}/.git/worktrees/wt-ctx-b"
+
+    # Unadopted worktree should NOT be updated
+    local content_unadopted
+    content_unadopted="$(cat "$wt_unadopted/.git")"
+    assert_equal "$content_unadopted" "gitdir: ${repo}/.git/worktrees/wt-ctx-unadopted"
+}
+
+@test "_wt_update_worktree_pointers all mode updates everything" {
+    local repo
+    repo=$(create_mock_repo "$BATS_TEST_TMPDIR/all-mode-repo")
+
+    create_branch "$repo" "branch-adopted"
+    create_branch "$repo" "branch-unadopted"
+    local wt_adopted="$BATS_TEST_TMPDIR/wt-all-adopted"
+    local wt_unadopted="$BATS_TEST_TMPDIR/wt-all-unadopted"
+    create_worktree "$repo" "$wt_adopted" "branch-adopted"
+    create_worktree "$repo" "$wt_unadopted" "branch-unadopted"
+    wt_adopted="$(cd "$wt_adopted" && pwd -P)"
+    wt_unadopted="$(cd "$wt_unadopted" && pwd -P)"
+
+    wt_mark_adopted "$wt_adopted"
+
+    # Move repo
+    local new_repo="$BATS_TEST_TMPDIR/moved-all-mode"
+    mv "$repo" "$new_repo"
+
+    run _wt_update_worktree_pointers "$new_repo" "all"
+    assert_success
+
+    # Both should be updated
+    local content_adopted content_unadopted
+    content_adopted="$(cat "$wt_adopted/.git")"
+    content_unadopted="$(cat "$wt_unadopted/.git")"
+    assert_equal "$content_adopted" "gitdir: ${new_repo}/.git/worktrees/wt-all-adopted"
+    assert_equal "$content_unadopted" "gitdir: ${new_repo}/.git/worktrees/wt-all-unadopted"
+}
+