@ainova-systems/intelligence 0.11.0 → 0.11.2

package/README.md

@@ -3,7 +3,7 @@
 **npm for AI agent intelligence.** One CLI that builds, versions and distributes the rules, agents and skills your AI coding tools run on — rendered natively for Claude Code, Cursor, GitHub Copilot, OpenAI Codex, Pi, OpenCode and `AGENTS.md`.
 
 ```bash
-npm install -g @ainova-systems/intelligence@next
+npm install -g @ainova-systems/intelligence
 
 cd your-project
 intelligence init

package/cli/commands/init.sh

@@ -12,6 +12,41 @@ source "$CLI_DIR/lib/cli-common.sh"
 
 targets_arg="" no_sync=0 content_dir="intelligence" bare=0
 targets_set=0 dir_set=0 bare_set=0 preview=0 apply=0 force=0
+onboarding_tx_active=0 onboarding_tx_root="" onboarding_tx_content=""
+
+onboarding_transaction_exit() {
+    local rc=$?
+    trap - EXIT
+    if [ "$onboarding_tx_active" -eq 1 ]; then
+        restore_onboarding_legacy_sources "$onboarding_tx_root" "$onboarding_tx_content"
+    fi
+    exit "$rc"
+}
+
+onboarding_transaction_begin() {
+    local tx_root="$1" tx_content="$2"
+    onboarding_quarantine_is_pending "$tx_root" "$tx_content" || return 0
+    onboarding_tx_root="$tx_root"
+    onboarding_tx_content="$tx_content"
+    onboarding_tx_active=1
+    trap onboarding_transaction_exit EXIT
+    quarantine_onboarding_legacy_sources "$tx_root" "$tx_content"
+}
+
+onboarding_transaction_rollback() {
+    trap - EXIT
+    if [ "$onboarding_tx_active" -eq 1 ]; then
+        restore_onboarding_legacy_sources "$onboarding_tx_root" "$onboarding_tx_content"
+    fi
+    onboarding_tx_active=0
+}
+
+onboarding_transaction_commit() {
+    local tx_root="$1" tx_content="$2"
+    complete_onboarding_quarantine "$tx_root" "$tx_content"
+    onboarding_tx_active=0
+    trap - EXIT
+}
 
 print_new_project_onboarding() {
     local heading="Intelligence ready"
@@ -22,6 +57,9 @@ print_new_project_onboarding() {
     if [ -n "${ONBOARDING_BACKUP_REL:-}" ]; then
         echo "  Existing AI instructions preserved:"
         echo "    $ONBOARDING_BACKUP_REL ($ONBOARDING_BACKUP_COUNT path(s))"
+        if [ "${ONBOARDING_LEGACY_COUNT:-0}" -gt 0 ]; then
+            echo "    Legacy root entry points were quarantined before the successful render."
+        fi
         if [ "$bare" -eq 0 ]; then
             echo "    The learn skill will migrate them before proposing backup removal."
         else
@@ -115,11 +153,13 @@ case "$IP_MODE" in
         ensure_manifest_gitignore "$IP_ROOT" "$IP_ROOT/intelligence.yaml"
         ensure_manifest_publisher_ignores "$IP_ROOT" "$IP_ROOT/intelligence.yaml"
         [ "$no_sync" -eq 1 ] && exit 0
+        content_dir="$(manifest_intelligence_dir "$IP_ROOT/intelligence.yaml")"
+        onboarding_transaction_begin "$IP_ROOT" "$content_dir"
         cd "$IP_ROOT"
         sync_rc=0
         bash "$CLI_DIR/commands/sync.sh" || sync_rc=$?
         if [ "$sync_rc" -ne 0 ]; then
-            content_dir="$(manifest_intelligence_dir "$IP_ROOT/intelligence.yaml")"
+            onboarding_transaction_rollback
             recovery_backup=""
             if [ -f "$IP_ROOT/$content_dir/_backup/manifest.tsv" ]; then
                 recovery_backup="; initial backup: $content_dir/_backup/manifest.tsv"
@@ -131,6 +171,7 @@ case "$IP_MODE" in
             echo "    $SYNC_PKG_STORE/skills/intelligence-learn-from-repository/SKILL.md" >&2
             echo "  and finalize this Intelligence setup$recovery_backup." >&2
         fi
+        [ "$sync_rc" -ne 0 ] || onboarding_transaction_commit "$IP_ROOT" "$content_dir"
         [ "$sync_rc" -ne 0 ] || report_tracked_managed_ignores "$IP_ROOT" "$IP_ROOT/intelligence.yaml"
         exit "$sync_rc"
         ;;
@@ -313,6 +354,7 @@ ensure_manifest_publisher_ignores "$root" "$manifest"
 echo "initialized: intelligence.yaml (targets:$(printf ' %s' $targets))"
 [ "$bare" -eq 1 ] && echo "  bare setup: no packages — engine meta-skills not installed"
 if [ "$no_sync" -eq 0 ]; then
+    onboarding_transaction_begin "$root" "$content_dir"
     cd "$root"
     sync_rc=0
     echo ""
@@ -320,6 +362,7 @@ if [ "$no_sync" -eq 0 ]; then
     echo "  Rendering enabled adapters in compact mode..."
     bash "$CLI_DIR/commands/sync.sh" --compact || sync_rc=$?
     if [ "$sync_rc" -ne 0 ]; then
+        onboarding_transaction_rollback
         echo "" >&2
         echo "=== Intelligence setup needs recovery ===" >&2
         echo "  No partial adapter update was kept; sync restored its pre-run outputs." >&2
@@ -332,6 +375,7 @@ if [ "$no_sync" -eq 0 ]; then
         fi
         exit "$sync_rc"
     fi
+    onboarding_transaction_commit "$root" "$content_dir"
     echo "=== Sync completed ==="
 fi
 

package/cli/internal/check.sh

@@ -117,8 +117,17 @@ while IFS= read -r target; do
                         || warn "adapter '$target' Git policy is missing '$value'"
                     ;;
                 include)
-                    grep -Fqx -- "!$value" "$IP_ROOT/.gitignore" 2>/dev/null \
-                        || warn "adapter '$target' Git policy is missing '!$value'"
+                    if ! grep -Fqx -- "!$value" "$IP_ROOT/.gitignore" 2>/dev/null; then
+                        warn "adapter '$target' Git policy is missing '!$value'"
+                    elif git -C "$IP_ROOT" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+                        if git -C "$IP_ROOT" check-ignore -q --no-index -- "$value"; then
+                            warn "adapter '$target' Git policy cannot re-include '$value' because another ignore rule still wins"
+                        else
+                            ignore_rc=$?
+                            [ "$ignore_rc" -eq 1 ] \
+                                || warn "adapter '$target' Git policy for '$value' could not be evaluated"
+                        fi
+                    fi
                     ;;
             esac
         fi

package/cli/lib/adapter-lifecycle.sh

@@ -31,3 +31,13 @@ adapter_contract_paths() {
     adapter_records_for "$root" "$content_dir" "$name" "$output" \
         | awk -F '\t' '$1 == "owned" || $1 == "managed" || $1 == "legacy" || $1 == "preserve" { print $2 }'
 }
+
+# Keep the record kind for onboarding. A single concrete path may be both an
+# adapter output and a legacy input (AGENTS.md is the important example), so
+# flattening the contract too early loses the information needed to quarantine
+# only legacy entry points.
+adapter_contract_onboarding_records() {
+    local root="$1" content_dir="$2" name="$3" output="$4"
+    adapter_records_for "$root" "$content_dir" "$name" "$output" \
+        | awk -F '\t' '$1 == "owned" || $1 == "managed" || $1 == "legacy" || $1 == "preserve" { print $1 "\t" $2 }'
+}

package/cli/lib/gitignore.sh

@@ -9,6 +9,42 @@ gitignore_add_line() {
     printf '%s\n' "$line" >> "$file"
 }
 
+gitignore_path_is_ignored() {
+    local root="$1" path="$2"
+    git -C "$root" rev-parse --is-inside-work-tree >/dev/null 2>&1 || return 2
+    git -C "$root" check-ignore -q --no-index -- "$path"
+}
+
+# Git cannot re-include a child of an excluded directory. Add explicit parent
+# reinclusions, then make sure both parent and child negations occur after any
+# pre-existing rule that still wins. The check-ignore probe also catches broad
+# patterns such as an old `.claude/` or `.cursor/**`, not just exact matches.
+gitignore_add_effective_include() {
+    local root="$1" value="${2#./}" dir parent="" part rc
+    dir="${value%/*}"
+    if [ "$dir" != "$value" ]; then
+        while IFS= read -r part; do
+            [ -n "$part" ] || continue
+            if [ -n "$parent" ]; then parent="$parent/$part"; else parent="$part"; fi
+            gitignore_add_line "$root" "!$parent/"
+            if gitignore_path_is_ignored "$root" "$parent/"; then
+                printf '!%s/\n' "$parent" >> "$root/.gitignore"
+            else
+                rc=$?
+                [ "$rc" -eq 1 ] || [ "$rc" -eq 2 ] || return "$rc"
+            fi
+        done < <(printf '%s\n' "$dir" | tr '/' '\n')
+    fi
+
+    gitignore_add_line "$root" "!$value"
+    if gitignore_path_is_ignored "$root" "$value"; then
+        printf '!%s\n' "$value" >> "$root/.gitignore"
+    else
+        rc=$?
+        [ "$rc" -eq 1 ] || [ "$rc" -eq 2 ] || return "$rc"
+    fi
+}
+
 ensure_gitignore_header() {
     local root="$1" file="$1/.gitignore"
     if [ ! -f "$file" ] || ! grep -Fqx '# Intelligence generated state and tool output' "$file"; then
@@ -36,7 +72,7 @@ ensure_target_gitignore() {
     while IFS=$'\t' read -r kind value; do
         case "$kind" in
             ignore)  gitignore_add_line "$root" "$value" ;;
-            include) gitignore_add_line "$root" "!$value" ;;
+            include) gitignore_add_effective_include "$root" "$value" ;;
         esac
     done <<< "$records"
 }
@@ -138,10 +174,11 @@ managed_gitignore_patterns() {
 }
 
 # Git does not apply ignore rules retroactively to files already in its index.
-# Name each affected path and print a command which only untracks it; the local
-# file remains available as migration input.
+# Name each affected path that still exists and print a command which only
+# untracks it. Quarantined legacy paths are already worktree deletions and must
+# not receive a misleading "keep the local copy" instruction.
 report_tracked_managed_ignores() {
-    local root="$1" manifest="$2" patterns tracked path quoted posix_quoted powershell_quoted
+    local root="$1" manifest="$2" patterns tracked path quoted posix_quoted powershell_quoted announced=0
     git -C "$root" rev-parse --is-inside-work-tree >/dev/null 2>&1 || return 0
     patterns="$(mktemp -t intelligence-gitignore-XXXXXX)"
     tracked="$(mktemp -t intelligence-tracked-XXXXXX)"
@@ -155,9 +192,13 @@ report_tracked_managed_ignores() {
         rm -f "$tracked"
         return 0
     }
-    echo "  Tracked files still bypass these .gitignore rules. Untrack them without deleting local copies:"
     while IFS= read -r -d '' path; do
         [ -n "$path" ] || continue
+        [ -e "$root/$path" ] || [ -L "$root/$path" ] || continue
+        if [ "$announced" -eq 0 ]; then
+            echo "  Tracked files still bypass these .gitignore rules. Untrack them without deleting local copies:"
+            announced=1
+        fi
         if [[ "$path" == *"'"* ]]; then
             # macOS still ships Bash 3.2; use portable sed rather than newer
             # parameter-replacement behavior for the embedded quote.

package/cli/lib/manifest.sh

@@ -114,11 +114,9 @@ target_set_enabled() {
             print
             next
         }
-        in_targets && target_missing && target_entry_seen && !in_target && /^[[:space:]]*$/ {
-            insert_missing_target()
-            print
-            next
-        }
+        # A blank line is not a target-section boundary: it may belong to a
+        # block scalar such as targets.agents.header. Wait until the target
+        # list reaches a top-level comment/key or EOF before inserting.
         in_targets && /^[A-Za-z]/ { flush_targets() }
         in_targets && /^  [A-Za-z]/ {
             target_entry_seen = 1

package/cli/lib/onboarding.sh

@@ -3,12 +3,22 @@
 # The snapshot is data-only and explicitly identifies itself as initial
 # onboarding state so recovery skills never mistake it for generated output.
 
-onboarding_source_paths() {
+onboarding_source_records() {
     local root="$1" content_dir="$2" targets="$3" target output
     for target in $targets; do
         output="$(default_target_output "$target")"
-        adapter_contract_paths "$root" "$content_dir" "$target" "$output"
-    done | awk 'NF && !seen[$0]++'
+        adapter_contract_onboarding_records "$root" "$content_dir" "$target" "$output"
+    done | awk -F '\t' 'NF == 2 && !seen[$1 SUBSEP $2]++'
+}
+
+onboarding_source_paths() {
+    onboarding_source_records "$1" "$2" "$3" \
+        | awk -F '\t' 'NF == 2 && !seen[$2]++ { print $2 }'
+}
+
+onboarding_legacy_paths() {
+    onboarding_source_records "$1" "$2" "$3" \
+        | awk -F '\t' '$1 == "legacy" && !seen[$2]++ { print $2 }'
 }
 
 onboarding_source_count() {
@@ -22,12 +32,13 @@ onboarding_source_count() {
 
 preserve_onboarding_sources() {
     local root="$1" content_dir="$2" targets="$3"
-    local rel src dest backup_rel backup stage target
+    local rel src dest backup_rel backup stage target legacy_count=0
     backup_rel="$content_dir/_backup"
     backup="$root/$backup_rel"
     ONBOARDING_BACKUP_COUNT="$(onboarding_source_count "$root" "$content_dir" "$targets")"
     ONBOARDING_BACKUP_REL=""
-    export ONBOARDING_BACKUP_COUNT ONBOARDING_BACKUP_REL
+    ONBOARDING_LEGACY_COUNT=0
+    export ONBOARDING_BACKUP_COUNT ONBOARDING_BACKUP_REL ONBOARDING_LEGACY_COUNT
     [ "$ONBOARDING_BACKUP_COUNT" -gt 0 ] || return 0
     [ ! -e "$backup" ] || die "onboarding backup already exists at $backup_rel - review or move it before rerunning init"
 
@@ -55,9 +66,72 @@ preserve_onboarding_sources() {
         printf 'path\t%s\n' "$rel" >> "$stage/manifest.tsv"
     done < <(onboarding_source_paths "$root" "$content_dir" "$targets")
 
+    while IFS= read -r rel; do
+        [ -e "$stage/$rel" ] || [ -L "$stage/$rel" ] || continue
+        printf 'legacy\t%s\n' "$rel" >> "$stage/manifest.tsv"
+        legacy_count=$((legacy_count + 1))
+    done < <(onboarding_legacy_paths "$root" "$content_dir" "$targets")
+
+    # This marker is deliberately outside manifest.tsv: the manifest is the
+    # immutable inventory, while the marker is short-lived transaction state.
+    [ "$legacy_count" -eq 0 ] || : > "$stage/.quarantine-pending"
+
     mv "$stage" "$backup"
     ensure_gitignore_header "$root"
     gitignore_add_line "$root" "$backup_rel/"
     ONBOARDING_BACKUP_REL="$backup_rel"
-    export ONBOARDING_BACKUP_REL
+    ONBOARDING_LEGACY_COUNT="$legacy_count"
+    export ONBOARDING_BACKUP_REL ONBOARDING_LEGACY_COUNT
+}
+
+onboarding_quarantine_is_pending() {
+    [ -f "$1/$2/_backup/.quarantine-pending" ]
+}
+
+onboarding_backup_legacy_paths() {
+    local manifest="$1/$2/_backup/manifest.tsv"
+    [ -f "$manifest" ] || return 0
+    awk -F '\t' '$1 == "legacy" && NF == 2 && !seen[$2]++ { print $2 }' "$manifest"
+}
+
+quarantine_onboarding_legacy_sources() {
+    local root="$1" content_dir="$2" rel src backup
+    onboarding_quarantine_is_pending "$root" "$content_dir" || return 0
+    backup="$root/$content_dir/_backup"
+    while IFS= read -r rel; do
+        [ -n "$rel" ] || continue
+        src="$root/$rel"
+        [ -e "$src" ] || [ -L "$src" ] || continue
+        [ -e "$backup/$rel" ] || [ -L "$backup/$rel" ] \
+            || die "initial backup is missing legacy path '$rel'"
+        if [ -d "$src" ] && [ ! -L "$src" ]; then
+            rm -rf -- "$src"
+        else
+            rm -f -- "$src"
+        fi
+    done < <(onboarding_backup_legacy_paths "$root" "$content_dir")
+}
+
+restore_onboarding_legacy_sources() {
+    local root="$1" content_dir="$2" rel src dest backup
+    onboarding_quarantine_is_pending "$root" "$content_dir" || return 0
+    backup="$root/$content_dir/_backup"
+    while IFS= read -r rel; do
+        [ -n "$rel" ] || continue
+        src="$backup/$rel"
+        [ -e "$src" ] || [ -L "$src" ] || continue
+        dest="$root/$rel"
+        if [ -d "$dest" ] && [ ! -L "$dest" ]; then
+            rm -rf -- "$dest"
+        else
+            rm -f -- "$dest"
+        fi
+        mkdir -p "$(dirname "$dest")"
+        cp -R "$src" "$dest" || die "failed to restore legacy onboarding path '$rel'"
+    done < <(onboarding_backup_legacy_paths "$root" "$content_dir")
+}
+
+complete_onboarding_quarantine() {
+    local marker="$1/$2/_backup/.quarantine-pending"
+    [ ! -f "$marker" ] || rm -f -- "$marker"
 }

package/engine/ENGINE_SHA

@@ -1 +1 @@
-88a9c74ddb8bee338671c7badbebd07669b668c0
+0230d83b42848492194f593ebdd387714371b682

package/engine/VERSION

@@ -1 +1 @@
-0.11.0
+0.11.2

package/engine/adapters/opencode.sh

@@ -39,8 +39,8 @@ adapter_contract_opencode() {
 
 # Strip frontmatter, return body only.
 # Direct call to the shared `strip_frontmatter` helper in lib/common.sh —
-# duplicating the awk block here would violate the "all parsing in common.sh"
-# convention (see CLAUDE.md / packages/sync/references/conventions.md).
+# duplicating the awk block here would fork frontmatter parsing, which the
+# convention keeps in one place.
 
 sync_opencode_skills() {
     local repo_root="$1"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ainova-systems/intelligence",
-  "version": "0.11.0",
+  "version": "0.11.2",
   "description": "Build, version and distribute AI agent intelligence across your organization — one CLI, versioned Intelligence Packages, and a sync engine for Claude Code, Cursor, Copilot, Codex, Pi and OpenCode.",
   "bin": {
     "intelligence": "bin/intelligence.js"

package/packages/sync/references/adapters.md

@@ -79,7 +79,7 @@ records through these helpers:
 | `adapter_contract_requires <name>` | Another target that must be enabled for a full sync |
 | `adapter_contract_owned <path>` | Path exclusively regenerated by this adapter |
 | `adapter_contract_managed <path>` | Shared or marker-managed path modified by this adapter |
-| `adapter_contract_legacy <path>` | Pre-Intelligence input preserved in the initial backup |
+| `adapter_contract_legacy <path>` | Pre-Intelligence input backed up, then quarantined for the first transactional render |
 | `adapter_contract_preserve <path>` | Settings or state preserved in place and included in the initial backup |
 | `adapter_contract_ignore <pattern>` | Exact `.gitignore` pattern managed on enable/init |
 | `adapter_contract_include <pattern>` | Exact negated `.gitignore` pattern managed on enable/init |

package/packages/sync/references/conventions.md

@@ -57,7 +57,7 @@ project:
   name: payments
   intelligence_dir: "intelligence"  # optional; this is the default
 
-schema_version: "0.11.0"
+schema_version: "0.11.1"
 
 sources:
   rules:
@@ -309,8 +309,10 @@ CLAUDE.md
 
 # Generated Claude and Cursor content; shared settings remain trackable
 .claude/*
+!.claude/
 !.claude/settings.json
 .cursor/*
+!.cursor/
 !.cursor/settings.json
 
 # Generated open-standard and Codex content
@@ -337,9 +339,11 @@ adapter output. Existing entries remain untouched and absent secondary ignore
 files are not created.
 
 An ignore rule does not untrack a file already in Git. After init or adapter
-enable, the CLI reports each affected tracked path with an exact
-`git rm --cached -- '<path>'` command; this preserves the local file while
-removing it from the index.
+enable, the CLI reports each affected tracked path that remains in the
+worktree with an exact `git rm --cached -- '<path>'` command; this preserves
+the local file while removing it from the index. Legacy root entry points
+quarantined into the initial backup are ordinary worktree deletions to review
+and stage, not candidates for `git rm --cached`.
 
 Before release, inspect the packager's actual file list. An npm `files`
 allowlist can force inclusion despite `.npmignore`, and a Dockerfile-specific
@@ -349,18 +353,18 @@ than inferring contents from Git status.
 
 `AGENTS.md` is the only shared root instruction entry point. During onboarding,
 move useful repository guidance from legacy root files such as `.cursorrules`
-and instruction-bearing `CLAUDE.md` into project-owned rules, verify the
-generated tool output, then remove the legacy file. Keep a root tool-specific
-file only when it contains genuinely local configuration that an adapter cannot
-represent; keep that exception gitignored rather than maintaining a second
-committed instruction source.
+and instruction-bearing `CLAUDE.md` out of their quarantined backup copies and
+into project-owned rules, then verify the generated tool output. Do not restore
+the original root monolith. Create a new root tool-specific file only when it
+contains genuinely local configuration that an adapter cannot represent; keep
+that exception gitignored rather than maintaining a second committed source.
 
 Before the first render, `intelligence init` preserves existing AI prompt paths
 under `<content-dir>/_backup/`. Its `manifest.tsv` labels the snapshot
-`initial-onboarding` and lists exact original paths. The context-learning skill
-first recovers or verifies CLI setup, then routes that state through
-`onboarding-migration.md` and repository learning. The backup remains until the
-user approves removal.
+`initial-onboarding`, lists exact original paths, and marks legacy entry points.
+Those legacy paths are quarantined only for the transactional first render; a
+failed render restores them, while a successful render leaves them inactive for
+repository learning. The backup remains until the user approves removal.
 
 ## Project-owned adapters
 

package/packages/sync/references/onboarding-migration.md

@@ -8,8 +8,10 @@ Git diff showing that the first sync replaced tracked tool output.
 
 When `<content-dir>/_backup/manifest.tsv` contains
 `state<TAB>initial-onboarding`, it is the authoritative inventory from before
-the first generated write. Read each `target` and `path` record before looking
-at current adapter output. If `path<TAB>AGENTS.md` is present, the backed-up
+the first generated write. Read each `target`, `path`, and `legacy` record
+before looking at current adapter output. A `legacy` record means the CLI
+quarantined that active entry point before the first successful render. If
+`path<TAB>AGENTS.md` is present, the backed-up
 file is the original custom project contract; keep following it while deciding
 how to migrate its durable guidance.
 
@@ -22,7 +24,8 @@ Treat these as migration inputs, not as current generated output:
 - Codex/Open Agent Skills, Pi rules/prompts, and OpenCode agents/commands;
 - scripts or documentation that describe an older sync path.
 
-Prefer the copy under `<content-dir>/_backup/`. If it is absent and the first
+Prefer the copy under `<content-dir>/_backup/`; do not restore quarantined root
+monoliths as active instructions. If the backup is absent and the first
 sync changed tracked files, inspect their pre-sync content read-only through
 Git (`git diff` and `git show HEAD:<path>`). Never restore old content directly
 into an adapter output directory.
@@ -60,7 +63,10 @@ Prefer updating an existing project-owned artifact to creating a sibling.
 Obtain approval per `CREATE`, `UPDATE`, `REMOVE`, or `KEEP` proposal. Apply
 project-owned source changes first, then run `intelligence sync` and
 `intelligence status --check`. Inspect the enabled targets to prove the
-migrated guidance arrived before removing old root instructions or tool files.
+migrated guidance arrived and verify quarantined old root instructions remain
+absent. Create a new root tool file only from a separately approved, genuinely
+machine-local subset that has no adapter representation; never restore the
+original instruction monolith.
 
 For every removed or renamed path, search all tracked files with `git ls-files`
 and report remaining references with file and line number. Apply an unambiguous
@@ -68,8 +74,10 @@ replacement directly; ask about narrative or otherwise ambiguous references.
 
 The CLI owns generated-output `.gitignore` entries and its blocks in existing
 `.vscodeignore`, `.npmignore`, and `.dockerignore` files. Verify them against
-the enabled adapters. Treat CLI-reported tracked ignored paths as unresolved
-until the user approves the exact `git rm --cached` commands. Preserve
+the enabled adapters. Treat CLI-reported tracked ignored paths that still exist
+locally as unresolved until the user approves the exact `git rm --cached`
+commands. A quarantined tracked legacy path is already a worktree deletion;
+review and stage that deletion normally instead of using `git rm --cached`. Preserve
 `AGENTS.md`, `.github/`, shared settings, and unrelated files under shared tool
 roots in Git, while excluding development-only Intelligence content from
 published artifacts. Inspect the packager's actual file list before release;

package/packages/sync/skills/intelligence-learn-from-repository/SKILL.md

@@ -19,7 +19,9 @@ mechanics; this skill supplies repository judgement.
 2. Inspect `<content-dir>/_backup/manifest.tsv`. A
    `state<TAB>initial-onboarding` record identifies the byte-preserved state
    from before Intelligence first wrote adapter output. Read every `path`
-   record and treat it as migration input, never generated output. A
+   record and treat it as migration input, never generated output. `legacy`
+   records name old entry points the CLI quarantined for the first successful
+   render; read their backup copies rather than restoring them. A
    `.intelligence/backup/config.yaml` file identifies a converted legacy
    Intelligence Sync project; use the converted sources and that config as
    migration evidence.
@@ -55,12 +57,12 @@ mechanics; this skill supplies repository judgement.
    materially covered by package content, propose `REMOVE` or a smaller
    `UPDATE`; require a content comparison, not merely a matching name.
 
-   Treat committed legacy root instructions such as `.cursorrules` and an
+   Treat backed-up legacy root instructions such as `.cursorrules` and an
    instruction-bearing `CLAUDE.md` as migration sources, not permanent parallel
-   entry points. Propose moving still-valid guidance into project-owned rules
-   and removing the legacy file after generated output is verified. Keep one
-   only for genuinely local, gitignored configuration an adapter cannot
-   represent. `AGENTS.md` remains the shared root instruction entry point.
+   entry points. Move still-valid shared guidance into project-owned rules; do
+   not restore the original monolith. Only when approved machine-local guidance
+   remains, create a small new gitignored `CLAUDE.md` from that subset after
+   migration. `AGENTS.md` remains the shared root instruction entry point.
 
    Review `.gitignore` and every existing `.vscodeignore`, `.npmignore`, and
    `.dockerignore` against the CLI-managed policy. Detect tracked files which
@@ -92,10 +94,12 @@ explains itself well.
    installed package content or generated tool output.
 10. Run `intelligence sync`, then `intelligence status --check`. Inspect the
     relevant generated `AGENTS.md`, Cursor rules, Claude rules, and any
-    packaging/build file list affected by ignore policy. Only then remove each
-    separately approved legacy root instruction file and rerun the consistency
-    check. Completion requires `IS_STATUS=ok`, a clean final check, and no
-    `onboarding is pending` header after accepted migration.
+    packaging/build file list affected by ignore policy. Verify quarantined
+    legacy root entry points remain absent. If the user approved a genuinely
+    machine-local exception, create a concise new gitignored root file from only
+    that content; never copy the backed-up monolith back. Completion requires
+    `IS_STATUS=ok`, a clean final check, and no `onboarding is pending` header
+    after accepted migration.
 11. Report what was created, updated, removed, or deliberately kept. Remind the
     user to commit source, manifest, lock, `AGENTS.md`, and shared `.github/`
     changes. Keep or remove the initial backup only by separate user approval.

package/packages/sync/skills/intelligence-sync/SKILL.md

@@ -18,3 +18,11 @@ context: fork
    commit its diff; never bypass the gate. A frozen restore refusal means the
    manifest and lock disagree or a pinned ref moved—report it without
    hand-copying package content.
+4. On a probable Intelligence defect, first ask whether to collect a sanitized
+   issue draft; collect nothing before approval and never use telemetry. Include
+   only approved CLI/version, expected/actual behavior, and safe error details—
+   no confidential or project-specific data. Show the draft and obtain separate
+   approval before filing. If declined, ask whether the opt-out is for this
+   session, a user/gitignored dev-project profile, or a shared team policy; save
+   it only with separate approval. Put team policy in a project-owned rule, and
+   never invent a profile path or infer the intended scope.