@dotdrelle/wiki-manager 0.15.41 → 0.15.43

package/src/shell/tui.tsx

@@ -381,7 +381,11 @@ function App(props: {
             input={state.input()}
             busy={state.busy()}
             chatMode={state.chatMode()}
-            chatFocused={!state.activeEditor()}
+            // The composer must lose focus for EVERY modal, not just the file
+            // editor. While the setup wizard was open the input stayed focused
+            // underneath it, so answering a wizard question also typed into the
+            // chat box at the bottom of the window.
+            chatFocused={!state.activeEditor() && screen() === 'main'}
             setInput={state.setInput}
             submit={submit}
             conversationRows={conversationRows()}
@@ -433,17 +437,33 @@ function App(props: {
             onSave={state.saveEditor}
             onCancel={state.closeEditor}
           />
+          {/*
+            Opaque backdrop, same treatment WizardApp gives the standalone
+            wizard. Without it the dialog floated over a live two-pane layout:
+            the panes showed through around its border and the whole thing read
+            as one garbled screen rather than as a modal.
+          */}
           {screen() === 'setup' ? (
-            <SetupWizard
-              mode="setup"
-              session={state.session}
+            <box
+              position="absolute"
+              left={0}
+              top={0}
               width={dimensions().width}
               height={dimensions().height}
-              initialRoute="workspace-name"
-              closeOnDone
-              onComplete={closeSetup}
-              onClose={closeSetup}
-            />
+              zIndex={39}
+              backgroundColor="#0B0D12"
+            >
+              <SetupWizard
+                mode="setup"
+                session={state.session}
+                width={dimensions().width}
+                height={dimensions().height}
+                initialRoute="workspace-name"
+                closeOnDone
+                onComplete={closeSetup}
+                onClose={closeSetup}
+              />
+            </box>
           ) : null}
         </box>
       }

package/wiki-workspace

@@ -70,13 +70,19 @@ parse_global_options() {
     export REQUESTS_CA_BUNDLE="$CACERT_PATH"
     export CURL_CA_BUNDLE="$CACERT_PATH"
   fi
-  set -- "${parsed[@]}"
+  # `${arr[@]}` on an EMPTY array is an unbound-variable error under `set -u`
+  # in bash <= 4.3 — which includes the /bin/bash 3.2 macOS still ships. Every
+  # optional array in this script therefore goes through the `${arr[@]+…}`
+  # guard (see compose_env_args, override_args, only_services…); these two were
+  # missed, so any invocation without a global option died on this line before
+  # reaching its subcommand.
+  set -- ${parsed[@]+"${parsed[@]}"}
   PARSED_ARGS=("$@")
 }
 
 PARSED_ARGS=()
 parse_global_options "$@"
-set -- "${PARSED_ARGS[@]}"
+set -- ${PARSED_ARGS[@]+"${PARSED_ARGS[@]}"}
 
 usage() {
   cat <<'EOF'
@@ -111,11 +117,33 @@ Commands:
   wiki <workspace> down             Stop all services for this workspace
   wiki <workspace> logs [args...]   Follow workspace service logs (tail 100 by default)
   wiki <workspace> serve [--open]   Start the web UI in foreground (--open launches browser)
+  wiki <workspace> reset [--dry-run] [--yes]
+                                    Empty the workspace, keeping .wikirc*, templates/ and
+                                    build-context/. Requires the services to be stopped.
   wiki <workspace> doctor           Run wiki doctor
   wiki <workspace> ingest           Run wiki ingest
   wiki <workspace> build            Run wiki build
   wiki <workspace> export           Run wiki export
-  wiki <workspace> run <args...>    Run arbitrary wiki CLI args
+  wiki <workspace> run <args...>    Run arbitrary wiki CLI args (see below)
+
+wiki CLI commands reachable through `wiki <workspace> run`:
+  history [--file <path>] [--limit <n>] [--json]
+                                    List workspace history commits (Git, workspace-local)
+  restore --run <sha> [--dry-run]   Revert every file changed by a run commit
+  restore --file <path> --to <sha> [--dry-run]
+                                    Restore one versioned file to a revision
+  query "<question>"                Answer from the wiki and its cited source notes
+  index                             Create or update the local vector index
+  refresh                           Regenerate only the stale deliverables
+  lint                              Static checks: dead links, orphans, stale deliverables
+  add-skill <source>                Install a workspace method (directory, .zip, HTTPS .zip)
+  config                            Show the effective .wikirc.yaml
+  group-concepts                    Regroup wiki concepts
+  doctor, ingest, build, export     Also available directly: wiki <workspace> <command>
+
+  History is versioned for wiki/, templates/, build-context/, deliverables/,
+  raw/ingested/ and .wiki/build-state.json only. A restore adds a commit rather
+  than rewriting history, and --dry-run previews it without writing.
 
 Configuration:
   workspaces/<workspace>/.env
@@ -338,7 +366,7 @@ agents_compose() {
     logs)
       local log_args=()
       read_lines_into_array log_args logs_args "$@"
-      _agents_dc logs "${log_args[@]}"
+      _agents_dc logs ${log_args[@]+"${log_args[@]}"}
       ;;
     pull)
       [[ $# -eq 0 ]] || die "agents pull does not take arguments"
@@ -1171,6 +1199,117 @@ run_wiki() {
   compose_for_workspace "$workspace" run --rm wiki "$@"
 }
 
+# What `wiki <workspace> reset` keeps: the METHOD. `.wikirc*` (provider, model,
+# retrieval, per-profile variants), `templates/` and `build-context/` describe
+# how this workspace produces; everything else is what it has produced, cached
+# or logged. `.git/` is kept too — the history from before the reset stays
+# reachable through `wiki restore`, which is the only cheap undo there is.
+#
+# `.env` is kept for a harder reason than method: it IS the workspace's
+# registration — ports, MCP auth tokens, WIKI_WORKSPACE_PATH. Deleting it makes
+# the very next line of reset_workspace (`run_wiki … init`, which starts with
+# need_workspace_env) die under `set -euo pipefail`, leaving the workspace
+# emptied and never re-scaffolded. And recovering it with `config` mints new
+# ports and tokens, silently invalidating every reference to the old ones
+# (mcp.endpoints.json among them). Nothing here may drop it.
+workspace_reset_keep() {
+  case "$1" in
+    .|..|.git) return 0 ;;
+    .env|.env.*) return 0 ;;
+    .wikirc*) return 0 ;;
+    templates|build-context) return 0 ;;
+    *) return 1 ;;
+  esac
+}
+
+# Destructive, and deliberately reachable ONLY from this CLI: no `wiki reset`
+# subcommand, no production job type, no MCP tool, no skill. Nothing Donna can
+# call may erase a workspace.
+#
+# It also stops after re-scaffolding. Chaining a sync or a build here would be
+# convenient exactly once and wrong every other time: refilling the workspace
+# is the user's decision, not a side effect of emptying it.
+reset_workspace() {
+  local workspace="$1"
+  shift
+  local assume_yes=0 dry_run=0
+  while [[ $# -gt 0 ]]; do
+    case "$1" in
+      --yes|-y) assume_yes=1 ;;
+      --dry-run) dry_run=1 ;;
+      *) die "reset accepts only --yes and --dry-run (got: $1)" ;;
+    esac
+    shift
+  done
+
+  need_workspace_env "$workspace"
+  local ws_path
+  ws_path="$(normalize_path "$(workspace_value "$workspace" WIKI_WORKSPACE_PATH)")"
+  [[ -d "$ws_path" ]] || die "workspace directory not found: $ws_path"
+
+  # A container still writing into the bind mount would recreate part of what
+  # we just erased, and leave files owned by another UID behind.
+  local running_services=()
+  read_lines_into_array running_services compose_for_workspace "$workspace" ps --status running --services
+  if [[ ${#running_services[@]} -gt 0 ]]; then
+    die "workspace services are still running (${running_services[*]}) — stop them first: wiki-workspace wiki $workspace down"
+  fi
+
+  local entry name
+  local removed=() kept=()
+  for entry in "$ws_path"/* "$ws_path"/.*; do
+    [[ -e "$entry" ]] || continue
+    name="$(basename "$entry")"
+    if workspace_reset_keep "$name"; then
+      [[ "$name" == "." || "$name" == ".." ]] || kept+=("$name")
+      continue
+    fi
+    removed+=("$name")
+  done
+
+  printf 'Workspace: %s (%s)\n' "$workspace" "$ws_path"
+  printf 'Keep:   %s\n' "${kept[*]:-(nothing)}"
+  printf 'Reset:  %s\n' "${removed[*]:-(nothing)}"
+
+  if [[ ${#removed[@]} -eq 0 ]]; then
+    printf 'Nothing to reset.\n'
+    return
+  fi
+
+  if [[ $dry_run -eq 1 ]]; then
+    printf 'Dry run: nothing was deleted. Re-run without --dry-run to apply.\n'
+    return
+  fi
+
+  if [[ $assume_yes -eq 0 ]]; then
+    [[ -t 0 ]] || die "reset needs a terminal to confirm — pass --yes for a non-interactive run"
+    printf 'This deletes the wiki, the deliverables and the sources. Type the workspace name to confirm (%s): ' "$workspace"
+    local answer=''
+    IFS= read -r answer || true
+    [[ "$answer" == "$workspace" ]] || die "reset aborted"
+  fi
+
+  for name in "${removed[@]}"; do
+    rm -rf -- "${ws_path:?}/$name" \
+      || die "could not remove $ws_path/$name — check file ownership (containers run as the node user), then retry"
+  done
+
+  # Puts the structure back: empty raw/wiki/deliverables trees, .wiki/skills,
+  # system-prompt, an empty profile, CLAUDE.md, .gitignore, and a fresh history
+  # baseline. `wiki init` never overwrites an existing file, so the kept
+  # `.wikirc*`, templates/ and build-context/ come through untouched.
+  run_wiki "$workspace" init
+
+  # The scaffold ships a demo brief in raw/untracked/. Reappearing here it would
+  # not read as a sample but as a pending source, and the next ingest would file
+  # it into the wiki as if the user had provided it.
+  rm -f -- "$ws_path/raw/untracked/demo-project-brief.md"
+
+  printf 'Reset done: %s\n' "$workspace"
+  printf 'Kept: %s\n' "${kept[*]:-(nothing)}"
+  printf 'Nothing was rebuilt. Bring the sources back when you decide to (e.g. /wiki-sync), then build.\n'
+}
+
 open_app_mode() {
   local url="$1"
   case "$(uname -s)" in
@@ -1452,7 +1591,7 @@ main() {
     logs)
       local log_args=()
       read_lines_into_array log_args logs_args "$@"
-      compose_for_workspace "$workspace" logs "${log_args[@]}" serve mcp-http production-mcp
+      compose_for_workspace "$workspace" logs ${log_args[@]+"${log_args[@]}"} serve mcp-http production-mcp
       ;;
     serve)
       local open_browser=0
@@ -1481,6 +1620,9 @@ main() {
 
       compose_for_workspace "$workspace" up serve
       ;;
+    reset)
+      reset_workspace "$workspace" "$@"
+      ;;
     doctor|ingest|build|export)
       run_wiki "$workspace" "$command" "$@"
       ;;