fix(scripts): 5 critical bugs from Phase 9 self-test

Bug 1: merge-mcp.sh fails on Cyrillic brain repo paths (jq fopen UTF-8 issue) → use --argjson with $(cat ...) instead of --slurpfile Bug 2: install.sh stripped only trailing .template, missed middle .template. → strip both '.template.' middle and '.template' trailing patterns Bug 3: manifest.json used brain-repo paths but verify.sh checked target paths → restructure manifest.files into {project-mode, user-mode, brain-internal} maps → verify.sh now picks map based on detected target mode Bug 4: make_backup_dir created empty backup dir, no file preservation → rsync/cp -r target tree to backup before any modifications Bug 5: brain's project-files/README.md overwrote consumer's README.md → install.sh now skips brain-internal READMEs in project/user copy loops Phase 9 self-test re-run on c:/tmp/test-consumer-fix: install + verify both PASS. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-05-11 01:24:52 +03:00
parent 97b5da32bf
commit 52584df34e
7 changed files with 277 additions and 35 deletions
@@ -5,28 +5,51 @@
  "required_tools": ["jq", "python", "git", "bash"],
  "optional_tools": ["gh", "gitleaks", "claude"],
  "files": {
-    "project-files/.mcp.json.template": "14dd78e8d4a795b85b444bbf7d51cf71b44c5614e3e041bf09d7eb9a6133f1d0",
-    "project-files/CLAUDE.md.template": "eaee69ec015b07527400f2579192cc1e634ae3192e91e668393600d6e440f6c9",
-    "project-files/README.md": "f91f0737ffffbd94f3fb84eeb856eb561b4759b62a57fcbf1c3b3f652a9505d8",
-    "project-files/docs/CHANGELOG_claude_md.template.md": "c9a004af5defab9dfe5408f85b37a9024cc91d9c898d27421297ee590ea8f9e9",
-    "project-files/docs/Plugin_stack_rules.template.md": "a6624d13bc1366c572d590a7ab125aaeea9cce091c00264797443b00eeefb864",
-    "project-files/docs/Pravila_raboty_Claude.template.md": "33adaba80b311269861777422f378438bfd08e1a6b1114c49836dd74a096f14c",
-    "project-files/docs/Tooling.template.md": "9ac1bde261de859760033d2cc22d8a848279ec540c409bf15b7735f39f8d8f99",
-    "project-files/docs/visualizations/hooks-skills-plugins-map.html": "ad61c5069ac25c70f23315bf7d4c9bd80d2f55380f27f5a95d0e93b80dfe2532",
-    "user-level-files/README.md": "1bca220f99df30ef1fbfb9314b8f5182784ba44e44e63e7ded10edd77e3c2cba",
-    "user-level-files/hooks/economy-mode-test.py": "8e42f2137ca79206b8b205334cdf89f1ac991932fe9e773c828c8a1496fa2403",
-    "user-level-files/hooks/economy-mode.py": "865f36bba142a717dec18fb1e5f055c17b157bd53cc5fdbc7ef1e8628b3c2f64",
-    "user-level-files/hooks/economy-postcompact.py": "7b96abde074e2f17e0e95d26d7a7fc02f7c4617c0d9787e359c80b6e695716e6",
-    "user-level-files/hooks/economy-self-check-test.py": "f0f668b88c684674473458d7364f54d537432dc1797ee939b948f635690289e0",
-    "user-level-files/hooks/economy-self-check.py": "962db87b1abd05a8f783aa6e93d482750c14970ed5ab5229ea58582550f884d7",
-    "user-level-files/hooks/economy-state-guard-test.py": "2c407af63a5356d051271ea9852485dd2265c593c6535f85c4055a6ebe480196",
-    "user-level-files/hooks/economy-state-guard.py": "bb5278e356c33b8f99f05ad184b2b8b8d11692407b8e6216be7b0cfe3e11457c",
-    "user-level-files/hooks/economy-verifier.py": "2b7431bcc1bf80179989e4f918a90de6b37627073cd04fa7a139757b18637a16",
-    "user-level-files/hooks/skill-check.py": "5f708f412d4d6ea66cd2f14ba119cf784b602d79052bbb976f904339421a09ad",
-    "user-level-files/hooks/skill-marker.py": "2d2ff205ae1390f87d1f8162e238729fa4d8c12340f02016ee1d54b3fff014a4",
-    "user-level-files/marketplaces.json": "9017c313525cb78f2078ba79fd974260cb8016f69dbb9a099dcff7b4153af300",
-    "user-level-files/mcp-user.template.json": "80cce6f971fa3dfca5533becab009060b703c914196a92ac3d6b2e3768b8b923",
-    "user-level-files/plugins-manifest.json": "1374cf8f4206b972a9ef5be6692773f2b8eaf1016588470a32588539f347f324",
-    "user-level-files/settings-fragment.json": "cbdda1e23034d0056db5165a85667d6a7d55de6e0629d7be4e9d9d7e4ebb4a7d"
+    "project-mode": {
+      ".mcp.json": "14dd78e8d4a795b85b444bbf7d51cf71b44c5614e3e041bf09d7eb9a6133f1d0",
+      "CLAUDE.md": "eaee69ec015b07527400f2579192cc1e634ae3192e91e668393600d6e440f6c9",
+      "docs/CHANGELOG_claude_md.md": "c9a004af5defab9dfe5408f85b37a9024cc91d9c898d27421297ee590ea8f9e9",
+      "docs/Plugin_stack_rules.md": "a6624d13bc1366c572d590a7ab125aaeea9cce091c00264797443b00eeefb864",
+      "docs/Pravila_raboty_Claude.md": "33adaba80b311269861777422f378438bfd08e1a6b1114c49836dd74a096f14c",
+      "docs/Tooling.md": "9ac1bde261de859760033d2cc22d8a848279ec540c409bf15b7735f39f8d8f99",
+      "docs/visualizations/hooks-skills-plugins-map.html": "ad61c5069ac25c70f23315bf7d4c9bd80d2f55380f27f5a95d0e93b80dfe2532"
+    },
+    "user-mode": {
+      "hooks/economy-mode-test.py": "8e42f2137ca79206b8b205334cdf89f1ac991932fe9e773c828c8a1496fa2403",
+      "hooks/economy-mode.py": "865f36bba142a717dec18fb1e5f055c17b157bd53cc5fdbc7ef1e8628b3c2f64",
+      "hooks/economy-postcompact.py": "7b96abde074e2f17e0e95d26d7a7fc02f7c4617c0d9787e359c80b6e695716e6",
+      "hooks/economy-self-check-test.py": "f0f668b88c684674473458d7364f54d537432dc1797ee939b948f635690289e0",
+      "hooks/economy-self-check.py": "962db87b1abd05a8f783aa6e93d482750c14970ed5ab5229ea58582550f884d7",
+      "hooks/economy-state-guard-test.py": "2c407af63a5356d051271ea9852485dd2265c593c6535f85c4055a6ebe480196",
+      "hooks/economy-state-guard.py": "bb5278e356c33b8f99f05ad184b2b8b8d11692407b8e6216be7b0cfe3e11457c",
+      "hooks/economy-verifier.py": "2b7431bcc1bf80179989e4f918a90de6b37627073cd04fa7a139757b18637a16",
+      "hooks/skill-check.py": "5f708f412d4d6ea66cd2f14ba119cf784b602d79052bbb976f904339421a09ad",
+      "hooks/skill-marker.py": "2d2ff205ae1390f87d1f8162e238729fa4d8c12340f02016ee1d54b3fff014a4"
+    },
+    "brain-internal": {
+      "project-files/.mcp.json.template": "14dd78e8d4a795b85b444bbf7d51cf71b44c5614e3e041bf09d7eb9a6133f1d0",
+      "project-files/CLAUDE.md.template": "eaee69ec015b07527400f2579192cc1e634ae3192e91e668393600d6e440f6c9",
+      "project-files/README.md": "f91f0737ffffbd94f3fb84eeb856eb561b4759b62a57fcbf1c3b3f652a9505d8",
+      "project-files/docs/CHANGELOG_claude_md.template.md": "c9a004af5defab9dfe5408f85b37a9024cc91d9c898d27421297ee590ea8f9e9",
+      "project-files/docs/Plugin_stack_rules.template.md": "a6624d13bc1366c572d590a7ab125aaeea9cce091c00264797443b00eeefb864",
+      "project-files/docs/Pravila_raboty_Claude.template.md": "33adaba80b311269861777422f378438bfd08e1a6b1114c49836dd74a096f14c",
+      "project-files/docs/Tooling.template.md": "9ac1bde261de859760033d2cc22d8a848279ec540c409bf15b7735f39f8d8f99",
+      "project-files/docs/visualizations/hooks-skills-plugins-map.html": "ad61c5069ac25c70f23315bf7d4c9bd80d2f55380f27f5a95d0e93b80dfe2532",
+      "user-level-files/README.md": "1bca220f99df30ef1fbfb9314b8f5182784ba44e44e63e7ded10edd77e3c2cba",
+      "user-level-files/hooks/economy-mode-test.py": "8e42f2137ca79206b8b205334cdf89f1ac991932fe9e773c828c8a1496fa2403",
+      "user-level-files/hooks/economy-mode.py": "865f36bba142a717dec18fb1e5f055c17b157bd53cc5fdbc7ef1e8628b3c2f64",
+      "user-level-files/hooks/economy-postcompact.py": "7b96abde074e2f17e0e95d26d7a7fc02f7c4617c0d9787e359c80b6e695716e6",
+      "user-level-files/hooks/economy-self-check-test.py": "f0f668b88c684674473458d7364f54d537432dc1797ee939b948f635690289e0",
+      "user-level-files/hooks/economy-self-check.py": "962db87b1abd05a8f783aa6e93d482750c14970ed5ab5229ea58582550f884d7",
+      "user-level-files/hooks/economy-state-guard-test.py": "2c407af63a5356d051271ea9852485dd2265c593c6535f85c4055a6ebe480196",
+      "user-level-files/hooks/economy-state-guard.py": "bb5278e356c33b8f99f05ad184b2b8b8d11692407b8e6216be7b0cfe3e11457c",
+      "user-level-files/hooks/economy-verifier.py": "2b7431bcc1bf80179989e4f918a90de6b37627073cd04fa7a139757b18637a16",
+      "user-level-files/hooks/skill-check.py": "5f708f412d4d6ea66cd2f14ba119cf784b602d79052bbb976f904339421a09ad",
+      "user-level-files/hooks/skill-marker.py": "2d2ff205ae1390f87d1f8162e238729fa4d8c12340f02016ee1d54b3fff014a4",
+      "user-level-files/marketplaces.json": "9017c313525cb78f2078ba79fd974260cb8016f69dbb9a099dcff7b4153af300",
+      "user-level-files/mcp-user.template.json": "80cce6f971fa3dfca5533becab009060b703c914196a92ac3d6b2e3768b8b923",
+      "user-level-files/plugins-manifest.json": "1374cf8f4206b972a9ef5be6692773f2b8eaf1016588470a32588539f347f324",
+      "user-level-files/settings-fragment.json": "cbdda1e23034d0056db5165a85667d6a7d55de6e0629d7be4e9d9d7e4ebb4a7d"
+    }
  }
 }
@@ -69,20 +69,47 @@ if [ "$dry_run" -eq 1 ]; then
    exit 0
 fi

-# Backup
+# Backup (Bug 4 fix): create backup dir AND actually copy existing target tree
+# into it BEFORE any modifications, so overwrites are recoverable.
 if [ "$force" -eq 0 ]; then
    backup=$(make_backup_dir "$target")
    log_info "Backup: $backup"
+    # Copy entire target tree into backup, excluding .git/ and .brain-backup-*
+    # rsync preferred; cp -r fallback for environments without rsync.
+    if command -v rsync >/dev/null 2>&1; then
+        rsync -a \
+            --exclude '.git/' \
+            --exclude '.brain-backup-*' \
+            "$target/" "$backup/" 2>/dev/null || true
+    else
+        # cp -r fallback: copy every top-level entry except .git and .brain-backup-*
+        for entry in "$target"/* "$target"/.[!.]* "$target"/..?*; do
+            [ -e "$entry" ] || continue
+            base=$(basename "$entry")
+            case "$base" in
+                .git|.brain-backup-*) continue ;;
+            esac
+            cp -r "$entry" "$backup/" 2>/dev/null || true
+        done
+    fi
 fi

 # Copy files per mode
 if [ "$mode" = "project" ]; then
    src="$BRAIN_ROOT/project-files"
    if [ -d "$src" ]; then
-        # Copy all files; strip .template suffix on the way
+        # Copy all files; strip .template suffix (BOTH middle and trailing — Bug 2 fix)
        while IFS= read -r -d '' f; do
            rel="${f#$src/}"
-            dst="$target/${rel%.template}"
+            # Bug 5: skip brain-internal README (it describes brain repo
+            # structure, not consumer content); consumer's own README stays.
+            case "$rel" in
+                README.md) continue ;;
+            esac
+            # Bug 2: strip both middle '.template.' and trailing '.template'
+            dst_rel="${rel//.template\./.}"
+            dst_rel="${dst_rel%.template}"
+            dst="$target/$dst_rel"
            mkdir -p "$(dirname "$dst")"
            cp "$f" "$dst"
        done < <(find "$src" -type f -print0)
@@ -99,6 +126,9 @@ elif [ "$mode" = "user" ]; then
    src="$BRAIN_ROOT/user-level-files"
    # Hooks
    [ -d "$src/hooks" ] && mkdir -p "$target/hooks" && cp "$src/hooks"/*.py "$target/hooks/" 2>/dev/null || true
+    # Bug 5: skip brain-internal README in user mode too (we never copy it
+    # explicitly above, but state it defensively for any future bulk copy).
+    # No-op currently — hooks are copied individually, README.md is not.
    # settings.json merge
    if [ -f "$src/settings-fragment.json" ]; then
        bash "$SCRIPT_DIR/lib/merge-settings.sh" "$target/settings.json" "$src/settings-fragment.json"
@@ -33,17 +33,19 @@ fi
 backup="${target}.bak.$(date +%s)"
 cp "$target" "$backup"

-# CORRECTION A: use --slurpfile to bind brain file to $brain (array of docs);
-# $brain[0] accesses the single document. This avoids the broken
-# "jq -s '.[0] | ... .[1].mcpServers'" form (which inside the inner pipe makes
-# .[1] index the object — runtime error "Cannot index object with number").
+# CORRECTION B (Bug 1 fix): use --argjson with shell-read content instead of
+# --slurpfile. jq on Windows MSYS2 cannot open paths with non-ASCII characters
+# (Cyrillic etc.) via its C-level fopen, but cat is a shell builtin/coreutil
+# that handles UTF-8 paths fine. --argjson takes a pre-parsed JSON string, so
+# this works regardless of path encoding.
 #
 # Merge semantics: target.mcpServers (or {} if missing) UNION brain.mcpServers,
 # with brain entries overriding on key collision (laravel-boost stays — brain
 # template doesn't define it; magic gets replaced if brain defines it).
+brain_content=$(cat "$brain_mcp")
 tmp="${target}.tmp"
-jq --slurpfile brain "$brain_mcp" \
-   '.mcpServers = ((.mcpServers // {}) + $brain[0].mcpServers)' \
+jq --argjson brain "$brain_content" \
+   '.mcpServers = ((.mcpServers // {}) + $brain.mcpServers)' \
   "$target" > "$tmp"

 # Validate
@@ -46,6 +46,83 @@ BRAIN_ROOT="$brain_dir" bash "$brain_dir/scripts/install.sh" --target="$tmpdir"

 rm -rf "$tmpdir" "$brain_dir"

+# Test 4: template strip handles BOTH middle .template. and trailing .template
+# Bug 2 regression: files like docs/CHANGELOG_claude_md.template.md must become
+# docs/CHANGELOG_claude_md.md, not be left with .template. in the middle.
+tmpdir=$(mktemp -d)
+mkdir "$tmpdir/docs"
+brain_dir=$(mktemp -d)
+mkdir -p "$brain_dir/project-files/docs" "$brain_dir/scripts/lib"
+echo "# trailing" > "$brain_dir/project-files/CLAUDE.md.template"
+echo "# middle" > "$brain_dir/project-files/docs/CHANGELOG_claude_md.template.md"
+echo '{"version":"brain-v1.0","files":{}}' > "$brain_dir/manifest.json"
+cp "$SCRIPT_DIR/install.sh" "$brain_dir/scripts/"
+cp "$SCRIPT_DIR/verify.sh" "$brain_dir/scripts/"
+cp "$SCRIPT_DIR/lib/common.sh" "$brain_dir/scripts/lib/"
+
+BRAIN_ROOT="$brain_dir" bash "$brain_dir/scripts/install.sh" --target="$tmpdir" --version=brain-v1.0 --with-plugins=no --with-mcp=no --skip-secrets --force >/dev/null 2>&1
+
+# Trailing .template stripped → CLAUDE.md
+[ -f "$tmpdir/CLAUDE.md" ] && assert_eq "yes" "yes" "template strip: trailing .template removed (CLAUDE.md)" || assert_eq "yes" "no" "template strip: trailing .template removed (CLAUDE.md)"
+
+# Middle .template. stripped → docs/CHANGELOG_claude_md.md
+[ -f "$tmpdir/docs/CHANGELOG_claude_md.md" ] && assert_eq "yes" "yes" "template strip: middle .template. removed (CHANGELOG_claude_md.md)" || assert_eq "yes" "no" "template strip: middle .template. removed (CHANGELOG_claude_md.md)"
+
+# Negative: file with .template. in middle must NOT exist with .template. still in name
+[ ! -f "$tmpdir/docs/CHANGELOG_claude_md.template.md" ] && assert_eq "yes" "yes" "template strip: no leftover .template. in name" || assert_eq "yes" "no" "template strip: no leftover .template. in name"
+
+rm -rf "$tmpdir" "$brain_dir"
+
+# Test 5: backup directory actually contains pre-existing consumer files (Bug 4)
+tmpdir=$(mktemp -d)
+mkdir "$tmpdir/docs"
+echo "ORIGINAL_README_CONTENT" > "$tmpdir/README.md"
+echo "ORIGINAL_MARKER" > "$tmpdir/CONSUMER_KEEP.txt"
+brain_dir=$(mktemp -d)
+mkdir -p "$brain_dir/project-files/docs" "$brain_dir/scripts/lib"
+echo "# brain template" > "$brain_dir/project-files/CLAUDE.md.template"
+echo '{"version":"brain-v1.0","files":{}}' > "$brain_dir/manifest.json"
+cp "$SCRIPT_DIR/install.sh" "$brain_dir/scripts/"
+cp "$SCRIPT_DIR/verify.sh" "$brain_dir/scripts/"
+cp "$SCRIPT_DIR/lib/common.sh" "$brain_dir/scripts/lib/"
+
+BRAIN_ROOT="$brain_dir" bash "$brain_dir/scripts/install.sh" --target="$tmpdir" --version=brain-v1.0 --with-plugins=no --with-mcp=no --skip-secrets >/dev/null 2>&1
+
+# Backup dir should exist
+backup_count=$(find "$tmpdir" -maxdepth 1 -type d -name ".brain-backup-*" | wc -l)
+assert_eq "1" "$backup_count" "backup: .brain-backup-<ts>/ created"
+
+# Backup should contain consumer's original README.md
+backup_dir=$(find "$tmpdir" -maxdepth 1 -type d -name ".brain-backup-*" | head -1)
+[ -f "$backup_dir/README.md" ] && assert_eq "yes" "yes" "backup: README.md preserved" || assert_eq "yes" "no" "backup: README.md preserved"
+backup_readme_content=$(cat "$backup_dir/README.md" 2>/dev/null || echo "")
+assert_eq "ORIGINAL_README_CONTENT" "$backup_readme_content" "backup: README.md content matches original"
+
+# Backup should also contain CONSUMER_KEEP.txt
+[ -f "$backup_dir/CONSUMER_KEEP.txt" ] && assert_eq "yes" "yes" "backup: CONSUMER_KEEP.txt preserved" || assert_eq "yes" "no" "backup: CONSUMER_KEEP.txt preserved"
+
+rm -rf "$tmpdir" "$brain_dir"
+
+# Test 6: consumer's pre-existing README.md is NOT overwritten by brain's project-files/README.md (Bug 5)
+tmpdir=$(mktemp -d)
+mkdir "$tmpdir/docs"
+echo "CONSUMER_ORIGINAL_README" > "$tmpdir/README.md"
+brain_dir=$(mktemp -d)
+mkdir -p "$brain_dir/project-files/docs" "$brain_dir/scripts/lib"
+echo "# brain template" > "$brain_dir/project-files/CLAUDE.md.template"
+echo "BRAIN_INTERNAL_README" > "$brain_dir/project-files/README.md"
+echo '{"version":"brain-v1.0","files":{}}' > "$brain_dir/manifest.json"
+cp "$SCRIPT_DIR/install.sh" "$brain_dir/scripts/"
+cp "$SCRIPT_DIR/verify.sh" "$brain_dir/scripts/"
+cp "$SCRIPT_DIR/lib/common.sh" "$brain_dir/scripts/lib/"
+
+BRAIN_ROOT="$brain_dir" bash "$brain_dir/scripts/install.sh" --target="$tmpdir" --version=brain-v1.0 --with-plugins=no --with-mcp=no --skip-secrets >/dev/null 2>&1
+
+readme_content=$(cat "$tmpdir/README.md")
+assert_eq "CONSUMER_ORIGINAL_README" "$readme_content" "consumer README.md preserved (not overwritten by brain's internal README.md)"
+
+rm -rf "$tmpdir" "$brain_dir"
+
 echo "---"
 echo "Failures: $FAILURES"
 exit $FAILURES
@@ -68,6 +68,29 @@ assert_eq "npx" "$pw" "project-mode: playwright added"

 rm -rf "$tmpdir"

+# Test 3: Cyrillic path (Bug 1 regression) — jq must handle non-ASCII paths
+# On Windows MSYS2 jq's fopen cannot open Cyrillic paths via --slurpfile.
+# Fix uses --argjson with $(cat …) — shell handles UTF-8 paths fine.
+cyr_dir="/tmp/тест-merge-$$"
+mkdir -p "$cyr_dir"
+cat > "$cyr_dir/brain.json" <<'EOF4'
+{"mcpServers":{"playwright":{"command":"npx","args":["-y","@playwright/mcp"]}}}
+EOF4
+echo '{"mcpServers":{"laravel-boost":{"command":"php"}}}' > "$cyr_dir/target.json"
+
+bash "$SCRIPT_DIR/lib/merge-mcp.sh" --mode=project "$cyr_dir/target.json" "$cyr_dir/brain.json" 2>/dev/null
+merge_exit=$?
+assert_eq "0" "$merge_exit" "cyrillic-path: merge-mcp.sh exits 0"
+
+if [ "$merge_exit" -eq 0 ]; then
+    pw=$(jq -r '.mcpServers.playwright.command' "$cyr_dir/target.json" 2>/dev/null || echo "")
+    assert_eq "npx" "$pw" "cyrillic-path: playwright merged from Cyrillic brain path"
+    lb=$(jq -r '.mcpServers["laravel-boost"].command' "$cyr_dir/target.json" 2>/dev/null || echo "")
+    assert_eq "php" "$lb" "cyrillic-path: laravel-boost preserved"
+fi
+
+rm -rf "$cyr_dir"
+
 echo "---"
 echo "Failures: $FAILURES"
 exit $FAILURES
@@ -25,6 +25,74 @@ BRAIN_ROOT="$brain_dir" bash "$SCRIPT_DIR/verify.sh" --target="$tmpdir" >/dev/nu
 assert_eq "0" "$?" "valid .brain-version returns exit 0"
 rm -rf "$tmpdir" "$brain_dir"

+# Test 3: project-mode verify with real consumer layout (Bug 3 regression)
+# Manifest uses project-mode section with target-relative paths.
+tmpdir=$(mktemp -d)
+echo "brain-v1.0" > "$tmpdir/.brain-version"
+echo "sha: deadbeef" >> "$tmpdir/.brain-version"
+mkdir -p "$tmpdir/docs"
+echo "consumer CLAUDE" > "$tmpdir/CLAUDE.md"
+echo "consumer pravila" > "$tmpdir/docs/Pravila_raboty_Claude.md"
+
+# Compute SHAs
+sha_claude=$(sha256sum "$tmpdir/CLAUDE.md" | cut -d' ' -f1)
+sha_pravila=$(sha256sum "$tmpdir/docs/Pravila_raboty_Claude.md" | cut -d' ' -f1)
+
+brain_dir=$(mktemp -d)
+cat > "$brain_dir/manifest.json" <<EOF7
+{
+  "version": "brain-v1.0",
+  "files": {
+    "project-mode": {
+      "CLAUDE.md": "$sha_claude",
+      "docs/Pravila_raboty_Claude.md": "$sha_pravila"
+    },
+    "user-mode": {},
+    "brain-internal": {}
+  }
+}
+EOF7
+
+BRAIN_ROOT="$brain_dir" bash "$SCRIPT_DIR/verify.sh" --target="$tmpdir" >/tmp/verify_test3.log 2>&1
+exit_code=$?
+assert_eq "0" "$exit_code" "project-mode: verify passes on consumer layout"
+
+# Verify it used the right section
+grep -q "Manifest section: project-mode" /tmp/verify_test3.log && \
+    assert_eq "yes" "yes" "project-mode: section auto-detected" || \
+    assert_eq "yes" "no" "project-mode: section auto-detected"
+
+rm -rf "$tmpdir" "$brain_dir" /tmp/verify_test3.log
+
+# Test 4: brain-internal verify when target is brain root itself
+brain_dir=$(mktemp -d)
+mkdir -p "$brain_dir/project-files"
+echo "brain-v1.0" > "$brain_dir/.brain-version"
+echo "sha: deadbeef" >> "$brain_dir/.brain-version"
+echo "internal" > "$brain_dir/project-files/CLAUDE.md.template"
+sha_internal=$(sha256sum "$brain_dir/project-files/CLAUDE.md.template" | cut -d' ' -f1)
+cat > "$brain_dir/manifest.json" <<EOF8
+{
+  "version": "brain-v1.0",
+  "files": {
+    "project-mode": {},
+    "user-mode": {},
+    "brain-internal": {
+      "project-files/CLAUDE.md.template": "$sha_internal"
+    }
+  }
+}
+EOF8
+
+BRAIN_ROOT="$brain_dir" bash "$SCRIPT_DIR/verify.sh" --target="$brain_dir" >/tmp/verify_test4.log 2>&1
+exit_code=$?
+assert_eq "0" "$exit_code" "brain-internal: verify passes on brain root"
+grep -q "Manifest section: brain-internal" /tmp/verify_test4.log && \
+    assert_eq "yes" "yes" "brain-internal: section auto-detected" || \
+    assert_eq "yes" "no" "brain-internal: section auto-detected"
+
+rm -rf "$brain_dir" /tmp/verify_test4.log
+
 echo "---"
 echo "Failures: $FAILURES"
 exit $FAILURES
@@ -40,8 +40,27 @@ log_info "Found .brain-version: $version"
 manifest="$BRAIN_ROOT/manifest.json"
 [ -f "$manifest" ] || { log_error "manifest.json missing in BRAIN_ROOT=$BRAIN_ROOT"; exit 1; }

-# Check 3: sha256 per file in manifest (если manifest содержит files)
-files_count=$(jq -r '(.files // {}) | length' "$manifest")
+# Bug 3 fix: manifest.files now has three sub-maps with target-relative paths:
+#   project-mode  — paths as they appear in consumer project target
+#   user-mode     — paths as they appear in ~/.claude/ target
+#   brain-internal — brain-repo paths (for self-verify when target == brain root)
+#
+# We pick the map based on detected target type:
+#   - target is the brain root itself (contains project-files/ AND manifest.json) → brain-internal
+#   - target is ~/.claude or has hooks/ or settings.json → user-mode
+#   - everything else (project-mode default)
+manifest_section=""
+if [ -d "$target/project-files" ] && [ -f "$target/manifest.json" ]; then
+    manifest_section="brain-internal"
+elif [ "$target" = "$HOME/.claude" ] || [ -d "$target/hooks" ] || [ -f "$target/settings.json" ]; then
+    manifest_section="user-mode"
+else
+    manifest_section="project-mode"
+fi
+log_info "Manifest section: $manifest_section"
+
+# Check 3: sha256 per file in chosen section
+files_count=$(jq -r --arg s "$manifest_section" '(.files[$s] // {}) | length' "$manifest")
 if [ "$files_count" -gt 0 ]; then
    log_info "Verifying $files_count file hashes..."
    while IFS= read -r entry; do
@@ -64,7 +83,7 @@ if [ "$files_count" -gt 0 ]; then
            log_error "SHA mismatch: $rel_path (expected $expected_sha, got $actual_sha)"
            exit 2
        fi
-    done < <(jq -c '(.files // {}) | to_entries[]' "$manifest")
+    done < <(jq -c --arg s "$manifest_section" '(.files[$s] // {}) | to_entries[]' "$manifest")
 fi

 # Check 4: strict secrets — no unresolved <<*>> placeholders