feat: implement 4 major SkillLoader gaps (cache/settings/shell/args)

1. Memoization/Caching
   - loadAll() now memoized (volatile loaded flag + double-check lock)
   - clearCache() invalidates and notifies listeners
   - Dynamic skills map for runtime-discovered skills
   - Conditional skills pending map with activation tracking
   - onSkillsChanged() listener registration (matches TS onDynamicSkillsLoaded)

2. Setting Source Enforcement
   - isSettingSourceEnabled() checks env CLAUDE_CODE_DISABLE_{SOURCE}
   - isEnvTruthy() for boolean env vars (1/true/yes)
   - CLAUDE_CODE_DISABLE_POLICY_SKILLS skips managed skills
   - getManagedSkillsPath() for policy-managed skill directory
   - Conditional loading per source (user/project/policy)

3. Shell Command Execution (PromptShellExecution)
   - Parse \\\! command \\\ code blocks and !\command\ inline syntax
   - Execute via bash or powershell per skill frontmatter shell field
   - Output replaces command placeholder in skill content
   - 30s timeout, proper error handling
   - MCP skills excluded from shell execution (security)

4. Argument Substitution (ArgumentSubstitution)
   - \ — full raw arguments string
   - \[n] — indexed access
   - \ — shorthand for indexed (bash-style)
   - Named arguments (\, \) mapped from frontmatter
   - Shell-quote aware parsing (handles quoted multi-word args)
   - Auto-append 'ARGUMENTS: ...' if no placeholder found
   - Progressive argument hints for UI

Also:
- Paths frontmatter: brace expansion (src/*.{ts,tsx} → [src/*.ts, src/*.tsx])
- splitPathInFrontmatter with comma-respecting-braces parsing
- activateConditionalSkillsForPaths() with proper activation model
- 17 new unit tests (104 total, 0 failures)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/main/java/com/claudecode/context/SkillLoader.java

@@ -9,6 +9,8 @@ import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.*;
+import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.function.Consumer;
 
 /**
  * Skills 技能加载器 —— 对应 claude-code/src/skills/loadSkillsDir.ts。
@@ -56,35 +58,175 @@ public class SkillLoader {
     /** 已加载文件的规范路径集合，用于 symlink 去重 */
     private final Set<Path> loadedCanonicalPaths = new HashSet<>();
 
+    // ==================== Memoization / Caching ====================
+
+    /** Whether skills have been loaded (memoization flag) */
+    private volatile boolean loaded = false;
+
+    /** Cached immutable skill list from last loadAll() */
+    private volatile List<Skill> cachedSkills = List.of();
+
+    /** Dynamic skills discovered from file paths during the session */
+    private final Map<String, Skill> dynamicSkills = new LinkedHashMap<>();
+
+    /** Conditional skills waiting for path activation */
+    private final Map<String, Skill> conditionalSkillsPending = new LinkedHashMap<>();
+
+    /** Names of skills that have been activated (survives cache clears within a session) */
+    private final Set<String> activatedConditionalSkillNames = new HashSet<>();
+
+    /** Listeners notified when skills are reloaded/changed */
+    private final List<Consumer<List<Skill>>> skillChangeListeners = new CopyOnWriteArrayList<>();
+
     public SkillLoader(Path projectDir) {
         this.projectDir = projectDir;
     }
 
     /**
-     * 扫描并加载所有技能文件
+     * 扫描并加载所有技能文件。
+     * 结果被缓存（memoized），后续调用返回缓存结果。
+     * 调用 {@link #clearCache()} 可强制重新加载。
      */
     public List<Skill> loadAll() {
-        skills.clear();
+        if (loaded) {
-        loadedCanonicalPaths.clear();
+            return cachedSkills;
+        }
+
+        synchronized (this) {
+            if (loaded) {
+                return cachedSkills;
+            }
+
+            skills.clear();
+            loadedCanonicalPaths.clear();
+
+            // 0. 内置技能
+            skills.addAll(BundledSkills.getAll());
+            log.debug("Loaded {} bundled skills", BundledSkills.getAll().size());
+
+            // --- Setting source checks (aligned with TS isSettingSourceEnabled) ---
+            boolean policyDisabled = isEnvTruthy("CLAUDE_CODE_DISABLE_POLICY_SKILLS");
+            boolean userSettingsEnabled = isSettingSourceEnabled("userSettings");
+            boolean projectSettingsEnabled = isSettingSourceEnabled("projectSettings");
+
+            // 1. Managed/policy skills (policySettings source)
+            if (!policyDisabled) {
+                Path managedSkillsDir = getManagedSkillsPath();
+                if (managedSkillsDir != null) {
+                    loadFromSkillsDirectory(managedSkillsDir, "policySettings");
+                }
+            }
+
+            // 2. 用户级技能（目录格式: skill-name/SKILL.md）
+            if (userSettingsEnabled) {
+                Path userSkillsDir = Path.of(System.getProperty("user.home"), ".claude", "skills");
+                loadFromSkillsDirectory(userSkillsDir, "user");
+            }
+
+            // 3. 项目级技能（目录格式: skill-name/SKILL.md）
+            if (projectSettingsEnabled) {
+                Path projectSkillsDir = projectDir.resolve(".claude").resolve("skills");
+                loadFromSkillsDirectory(projectSkillsDir, "project");
+            }
+
+            // 4. 命令目录（支持目录格式 + 单文件格式 + 递归子目录）
+            Path commandsDir = projectDir.resolve(".claude").resolve("commands");
+            loadFromCommandsDirectory(commandsDir, "command");
+
+            // Separate conditional and unconditional skills
+            List<Skill> unconditional = new ArrayList<>();
+            for (Skill skill : skills) {
+                if (skill.isConditional() && !activatedConditionalSkillNames.contains(skill.name())) {
+                    conditionalSkillsPending.put(skill.name(), skill);
+                } else {
+                    unconditional.add(skill);
+                }
+            }
+
+            if (!conditionalSkillsPending.isEmpty()) {
+                log.debug("{} conditional skills stored (activated when matching files are touched)",
+                        conditionalSkillsPending.size());
+            }
 
-        // 0. 内置技能
+            log.debug("Loaded {} skills in total ({} unconditional, {} conditional)",
-        skills.addAll(BundledSkills.getAll());
+                    skills.size(), unconditional.size(), conditionalSkillsPending.size());
-        log.debug("Loaded {} bundled skills", BundledSkills.getAll().size());
 
-        // 1. 用户级技能（目录格式: skill-name/SKILL.md）
+            cachedSkills = Collections.unmodifiableList(unconditional);
-        Path userSkillsDir = Path.of(System.getProperty("user.home"), ".claude", "skills");
+            loaded = true;
-        loadFromSkillsDirectory(userSkillsDir, "user");
 
-        // 2. 项目级技能（目录格式: skill-name/SKILL.md）
+            return cachedSkills;
-        Path projectSkillsDir = projectDir.resolve(".claude").resolve("skills");
+        }
-        loadFromSkillsDirectory(projectSkillsDir, "project");
+    }
 
-        // 3. 命令目录（支持目录格式 + 单文件格式 + 递归子目录）
+    /**
-        Path commandsDir = projectDir.resolve(".claude").resolve("commands");
+     * Clear the memoization cache. Next call to {@link #loadAll()} will rescan directories.
-        loadFromCommandsDirectory(commandsDir, "command");
+     * Also clears conditional skills pending state.
+     * Corresponds to TS clearSkillCaches().
+     */
+    public void clearCache() {
+        synchronized (this) {
+            loaded = false;
+            cachedSkills = List.of();
+            skills.clear();
+            loadedCanonicalPaths.clear();
+            conditionalSkillsPending.clear();
+            activatedConditionalSkillNames.clear();
+            dynamicSkills.clear();
+        }
+        notifyListeners();
+    }
 
-        log.debug("Loaded {} skills in total", skills.size());
+    /**
-        return Collections.unmodifiableList(skills);
+     * Register a listener that is notified when skills are reloaded.
+     * Corresponds to TS onDynamicSkillsLoaded().
+     */
+    public void onSkillsChanged(Consumer<List<Skill>> listener) {
+        skillChangeListeners.add(listener);
+    }
+
+    private void notifyListeners() {
+        List<Skill> current = getSkills();
+        for (Consumer<List<Skill>> listener : skillChangeListeners) {
+            try {
+                listener.accept(current);
+            } catch (Exception e) {
+                log.warn("Skill change listener failed: {}", e.getMessage());
+            }
+        }
+    }
+
+    // ==================== Setting Source Helpers ====================
+
+    /**
+     * Check if an environment variable is truthy (1, true, yes).
+     * Corresponds to TS isEnvTruthy().
+     */
+    private static boolean isEnvTruthy(String name) {
+        String val = System.getenv(name);
+        if (val == null) val = System.getProperty(name);
+        if (val == null) return false;
+        return "1".equals(val) || "true".equalsIgnoreCase(val) || "yes".equalsIgnoreCase(val);
+    }
+
+    /**
+     * Check if a setting source is enabled.
+     * Default: all sources enabled unless explicitly disabled via environment.
+     * Corresponds to TS isSettingSourceEnabled().
+     */
+    private static boolean isSettingSourceEnabled(String source) {
+        // CLAUDE_CODE_DISABLE_{SOURCE} → disables that source
+        String envKey = "CLAUDE_CODE_DISABLE_" + source.toUpperCase().replace("SETTINGS", "_SETTINGS");
+        return !isEnvTruthy(envKey);
+    }
+
+    /**
+     * Get managed/policy skills directory path (if configured).
+     */
+    private static Path getManagedSkillsPath() {
+        String managedPath = System.getenv("CLAUDE_CODE_MANAGED_PATH");
+        if (managedPath == null) managedPath = System.getProperty("claude.managed.path");
+        if (managedPath == null) return null;
+        return Path.of(managedPath, ".claude", "skills");
     }
 
     /**
@@ -277,7 +419,7 @@ public class SkillLoader {
             log.warn("Invalid shell '{}' in {}, ignoring (use 'bash' or 'powershell')", shell, path);
             shell = null;
         }
-        List<String> paths = fmStringList(fm, "paths");
+        List<String> paths = parseSkillPaths(fm);
         String argumentHint = fmString(fm, "argument-hint", null);
         List<String> arguments = fmStringList(fm, "arguments");
         String version = fmString(fm, "version", null);
@@ -405,6 +547,102 @@ public class SkillLoader {
         return "";
     }
 
+    // ==================== Paths Parsing (brace expansion) ====================
+
+    /**
+     * Parse and validate paths frontmatter field with brace expansion.
+     * Corresponds to TS parseSkillPaths() + splitPathInFrontmatter().
+     *
+     * @return parsed path patterns, or null if no paths / all match-all
+     */
+    private List<String> parseSkillPaths(Map<String, Object> fm) {
+        Object val = fm.get("paths");
+        if (val == null) return null;
+
+        List<String> raw = splitPathInFrontmatter(val);
+        List<String> patterns = raw.stream()
+                .map(p -> p.endsWith("/**") ? p.substring(0, p.length() - 3) : p)
+                .filter(p -> !p.isEmpty())
+                .toList();
+
+        // If all patterns are ** (match-all), treat as no paths
+        if (patterns.isEmpty() || patterns.stream().allMatch(p -> p.equals("**"))) {
+            return null;
+        }
+        return patterns;
+    }
+
+    /**
+     * Split a comma-separated string (or YAML list) and expand brace patterns.
+     * Commas inside braces are not treated as separators.
+     * Corresponds to TS splitPathInFrontmatter().
+     */
+    @SuppressWarnings("unchecked")
+    private List<String> splitPathInFrontmatter(Object input) {
+        if (input instanceof List) {
+            return ((List<Object>) input).stream()
+                    .flatMap(item -> splitPathInFrontmatter(item).stream())
+                    .toList();
+        }
+        if (!(input instanceof String s)) {
+            return List.of();
+        }
+
+        // Split by comma while respecting braces
+        List<String> parts = new ArrayList<>();
+        StringBuilder current = new StringBuilder();
+        int braceDepth = 0;
+
+        for (int i = 0; i < s.length(); i++) {
+            char c = s.charAt(i);
+            if (c == '{') {
+                braceDepth++;
+                current.append(c);
+            } else if (c == '}') {
+                braceDepth--;
+                current.append(c);
+            } else if (c == ',' && braceDepth == 0) {
+                String trimmed = current.toString().strip();
+                if (!trimmed.isEmpty()) parts.add(trimmed);
+                current.setLength(0);
+            } else {
+                current.append(c);
+            }
+        }
+        String trimmed = current.toString().strip();
+        if (!trimmed.isEmpty()) parts.add(trimmed);
+
+        // Expand brace patterns
+        return parts.stream()
+                .filter(p -> !p.isEmpty())
+                .flatMap(p -> expandBraces(p).stream())
+                .toList();
+    }
+
+    /**
+     * Expand brace patterns in a glob string.
+     * e.g. "src/*.{ts,tsx}" → ["src/*.ts", "src/*.tsx"]
+     */
+    private List<String> expandBraces(String pattern) {
+        // Find the first brace group
+        int braceStart = pattern.indexOf('{');
+        if (braceStart < 0) return List.of(pattern);
+
+        int braceEnd = pattern.indexOf('}', braceStart);
+        if (braceEnd < 0) return List.of(pattern);
+
+        String prefix = pattern.substring(0, braceStart);
+        String alternatives = pattern.substring(braceStart + 1, braceEnd);
+        String suffix = pattern.substring(braceEnd + 1);
+
+        List<String> expanded = new ArrayList<>();
+        for (String alt : alternatives.split(",")) {
+            String combined = prefix + alt.strip() + suffix;
+            expanded.addAll(expandBraces(combined));
+        }
+        return expanded;
+    }
+
     // ==================== Gitignore 过滤 & Symlink 去重 ====================
 
     /**
@@ -447,32 +685,89 @@ public class SkillLoader {
     }
 
     /**
-     * 获取已加载的技能列表
+     * 获取已加载的技能列表（包含动态发现的技能）
      */
     public List<Skill> getSkills() {
-        return Collections.unmodifiableList(skills);
+        List<Skill> base = cachedSkills;
+        if (dynamicSkills.isEmpty()) {
+            return base;
+        }
+        List<Skill> combined = new ArrayList<>(base);
+        combined.addAll(dynamicSkills.values());
+        return Collections.unmodifiableList(combined);
     }
 
     /**
-     * 按名称查找技能（精确匹配，不区分大小写）
+     * 按名称查找技能（精确匹配，不区分大小写，搜索所有技能含动态）
      */
     public Optional<Skill> findByName(String name) {
-        return skills.stream()
+        return getSkills().stream()
                 .filter(s -> s.name().equalsIgnoreCase(name))
                 .findFirst();
     }
 
     /**
-     * 获取非条件技能（始终激活的技能）
+     * 获取非条件技能（始终激活的技能 + 已激活的动态技能）
      */
     public List<Skill> getUnconditionalSkills() {
-        return skills.stream()
+        return getSkills().stream()
                 .filter(s -> !s.isConditional())
                 .toList();
     }
 
     /**
-     * 获取匹配指定文件路径的条件技能。
+     * Get the number of pending conditional skills (for testing/debugging).
+     */
+    public int getConditionalSkillCount() {
+        return conditionalSkillsPending.size();
+    }
+
+    /**
+     * Activate conditional skills whose path patterns match the given file paths.
+     * Activated skills are moved to the dynamic skills map.
+     * Corresponds to TS activateConditionalSkillsForPaths().
+     *
+     * @param filePaths 当前操作的文件路径列表
+     * @return 新激活的技能名称列表
+     */
+    public List<String> activateConditionalSkillsForPaths(List<String> filePaths) {
+        if (filePaths == null || filePaths.isEmpty() || conditionalSkillsPending.isEmpty()) {
+            return List.of();
+        }
+
+        List<String> activated = new ArrayList<>();
+        Iterator<Map.Entry<String, Skill>> it = conditionalSkillsPending.entrySet().iterator();
+        while (it.hasNext()) {
+            Map.Entry<String, Skill> entry = it.next();
+            Skill skill = entry.getValue();
+            if (skill.paths() == null) continue;
+
+            for (String pattern : skill.paths()) {
+                for (String filePath : filePaths) {
+                    String relative = projectDir != null
+                            ? projectDir.relativize(Path.of(filePath).toAbsolutePath()).toString().replace('\\', '/')
+                            : filePath.replace('\\', '/');
+                    if (matchGlob(pattern, relative)) {
+                        dynamicSkills.put(skill.name(), skill);
+                        activatedConditionalSkillNames.add(skill.name());
+                        activated.add(skill.name());
+                        it.remove();
+                        log.debug("Activated conditional skill '{}' (matched path: {})", skill.name(), relative);
+                        break;
+                    }
+                }
+                if (activated.contains(entry.getKey())) break;
+            }
+        }
+
+        if (!activated.isEmpty()) {
+            notifyListeners();
+        }
+        return activated;
+    }
+
+    /**
+     * 获取匹配指定文件路径的条件技能（不修改状态，仅查询）。
      * 对应 TS discoverSkillDirsForPaths()。
      *
      * @param filePaths 当前编辑的文件路径列表
@@ -481,9 +776,13 @@ public class SkillLoader {
     public List<Skill> getConditionalSkillsForPaths(List<String> filePaths) {
         if (filePaths == null || filePaths.isEmpty()) return List.of();
 
-        return skills.stream()
+        // Search both pending conditional skills and all loaded conditional skills
-                .filter(Skill::isConditional)
+        List<Skill> allConditional = new ArrayList<>(conditionalSkillsPending.values());
+        allConditional.addAll(getSkills().stream().filter(Skill::isConditional).toList());
+
+        return allConditional.stream()
                 .filter(skill -> {
+                    if (skill.paths() == null) return false;
                     for (String pattern : skill.paths()) {
                         for (String filePath : filePaths) {
                             if (matchGlob(pattern, filePath)) {

src/main/java/com/claudecode/tool/impl/SkillTool.java

@@ -4,6 +4,8 @@ import com.claudecode.context.SkillLoader;
 import com.claudecode.context.SkillLoader.Skill;
 import com.claudecode.tool.Tool;
 import com.claudecode.tool.ToolContext;
+import com.claudecode.util.ArgumentSubstitution;
+import com.claudecode.util.PromptShellExecution;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -116,13 +118,13 @@ public class SkillTool implements Tool {
         log.info("Executing skill: {} [{}] context={}", skill.name(), skill.source(), skill.context());
 
         // Build skill execution prompt
-        String skillPrompt = buildSkillPrompt(skill, arguments);
+        String skillPrompt = buildSkillPrompt(skill, arguments, context);
 
         // Check if skill should be forked (sub-agent) or inline
         if (!skill.isForked()) {
             // Inline execution: return the skill prompt for the current agent to follow
             return "📋 Skill '" + skill.userFacingName() + "' loaded (inline mode).\n\n"
-                    + "Follow these instructions:\n\n" + skill.content();
+                    + "Follow these instructions:\n\n" + skillPrompt;
         }
 
         // Forked execution: execute via agent factory (same as AgentTool)
@@ -160,9 +162,10 @@ public class SkillTool implements Tool {
 
     /**
      * Build the full prompt for skill execution.
-     * Supports argument substitution (${ARGUMENT_NAME}, ${CLAUDE_SKILL_DIR}, ${CLAUDE_SESSION_ID}).
+     * Supports argument substitution ($ARGUMENTS, $n, $name, ${CLAUDE_SKILL_DIR}, ${CLAUDE_SESSION_ID}).
+     * Supports embedded shell command execution (!`cmd` and ```! cmd ```).
      */
-    private String buildSkillPrompt(Skill skill, String arguments) {
+    private String buildSkillPrompt(Skill skill, String arguments, ToolContext context) {
         StringBuilder sb = new StringBuilder();
         sb.append("You are executing a skill: ").append(skill.userFacingName()).append("\n\n");
 
@@ -188,14 +191,45 @@ public class SkillTool implements Tool {
             sb.append("Disallowed tools: ").append(String.join(", ", skill.disallowedTools())).append("\n");
         }
 
-        // Inject skill content with argument substitution
+        // Build content with argument substitution
         String content = skill.content();
-        content = substituteArguments(content, arguments, skill);
+
+        // Prepend base directory if available (matches TS behavior)
+        Path skillDir = skill.filePath() != null ? skill.filePath().getParent() : null;
+        if (skillDir != null) {
+            content = "Base directory for this skill: " + skillDir + "\n\n" + content;
+        }
+
+        // Argument substitution using new utility (matches TS substituteArguments)
+        List<String> argNames = skill.arguments() != null ? skill.arguments() : List.of();
+        content = ArgumentSubstitution.substituteArguments(content, arguments, true, argNames);
+
+        // Replace ${CLAUDE_SKILL_DIR} with normalized path
+        if (skillDir != null) {
+            String skillDirStr = skillDir.toString();
+            // Normalize backslashes to forward slashes on Windows (matches TS)
+            if (System.getProperty("os.name", "").toLowerCase().contains("win")) {
+                skillDirStr = skillDirStr.replace('\\', '/');
+            }
+            content = content.replace("${CLAUDE_SKILL_DIR}", skillDirStr);
+        }
+
+        // Replace ${CLAUDE_SESSION_ID}
+        content = content.replace("${CLAUDE_SESSION_ID}",
+                System.getProperty("claude.session.id", "default-session"));
+
+        // Execute embedded shell commands (!`cmd` and ```! cmd ```)
+        // Security: skip for MCP skills (remote/untrusted)
+        if (!"mcp".equals(skill.source())) {
+            Path workDir = context != null ? context.getWorkDir() : skillDir;
+            content = PromptShellExecution.executeShellCommandsInPrompt(content, skill.shell(), workDir);
+        }
+
         sb.append("## Skill Instructions\n\n");
         sb.append(content).append("\n\n");
 
-        // Inject arguments
+        // Inject arguments section (for forked context only, inline already has content)
-        if (arguments != null && !arguments.isBlank()) {
+        if (arguments != null && !arguments.isBlank() && skill.isForked()) {
             sb.append("## User Arguments\n\n");
             sb.append(arguments).append("\n\n");
         }
@@ -211,41 +245,6 @@ public class SkillTool implements Tool {
         return sb.toString();
     }
 
-    /**
-     * Argument substitution — replaces ${ARGUMENT_NAME}, ${CLAUDE_SKILL_DIR}, ${CLAUDE_SESSION_ID}.
-     * Corresponds to TS substituteArguments() + template variables.
-     */
-    private String substituteArguments(String content, String arguments, Skill skill) {
-        if (content == null) return "";
-
-        // Replace ${CLAUDE_SKILL_DIR} with the skill's directory
-        if (skill.filePath() != null) {
-            Path skillDir = skill.filePath().getParent();
-            if (skillDir != null) {
-                content = content.replace("${CLAUDE_SKILL_DIR}", skillDir.toString());
-            }
-        }
-
-        // Replace ${CLAUDE_SESSION_ID} with a session identifier
-        content = content.replace("${CLAUDE_SESSION_ID}",
-                System.getProperty("claude.session.id", "default-session"));
-
-        // Replace generic ${ARGUMENTS} or positional args
-        if (arguments != null && !arguments.isBlank()) {
-            content = content.replace("${ARGUMENTS}", arguments);
-
-            // Parse named arguments from skill definition
-            if (skill.arguments() != null) {
-                String[] argValues = arguments.split("\\s+", skill.arguments().size());
-                for (int i = 0; i < skill.arguments().size() && i < argValues.length; i++) {
-                    content = content.replace("${" + skill.arguments().get(i) + "}", argValues[i]);
-                }
-            }
-        }
-
-        return content;
-    }
-
     /**
      * Partial name match for skills.
      */

src/main/java/com/claudecode/util/ArgumentSubstitution.java

@@ -0,0 +1,190 @@
+package com.claudecode.util;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Argument substitution for skill/command prompts.
+ * Aligns with claude-code/src/utils/argumentSubstitution.ts.
+ * <p>
+ * Supports:
+ * <ul>
+ *   <li>$ARGUMENTS — replaced with the full arguments string</li>
+ *   <li>$ARGUMENTS[0], $ARGUMENTS[1], … — indexed access</li>
+ *   <li>$0, $1, … — shorthand for $ARGUMENTS[n]</li>
+ *   <li>Named arguments ($foo, $bar) — mapped from frontmatter argument names</li>
+ *   <li>${CLAUDE_SKILL_DIR}, ${CLAUDE_SESSION_ID} — special variables</li>
+ * </ul>
+ */
+public final class ArgumentSubstitution {
+
+    private ArgumentSubstitution() {}
+
+    // $ARGUMENTS[n]
+    private static final Pattern INDEXED_PATTERN = Pattern.compile("\\$ARGUMENTS\\[(\\d+)]");
+    // $n (not followed by word chars, to avoid matching $100foo)
+    private static final Pattern SHORTHAND_PATTERN = Pattern.compile("\\$(\\d+)(?!\\w)");
+
+    /**
+     * Parse a raw argument string into individual arguments with shell-quote awareness.
+     * Handles double-quoted and single-quoted strings.
+     * <p>
+     * Examples:
+     * <pre>
+     *   "foo bar baz"           → ["foo", "bar", "baz"]
+     *   "foo \"hello world\" z" → ["foo", "hello world", "z"]
+     *   "foo 'hello world' z"   → ["foo", "hello world", "z"]
+     * </pre>
+     */
+    public static List<String> parseArguments(String args) {
+        if (args == null || args.isBlank()) {
+            return List.of();
+        }
+
+        List<String> result = new ArrayList<>();
+        StringBuilder current = new StringBuilder();
+        boolean inDoubleQuote = false;
+        boolean inSingleQuote = false;
+        boolean escaped = false;
+
+        for (int i = 0; i < args.length(); i++) {
+            char c = args.charAt(i);
+
+            if (escaped) {
+                current.append(c);
+                escaped = false;
+                continue;
+            }
+
+            if (c == '\\' && !inSingleQuote) {
+                escaped = true;
+                continue;
+            }
+
+            if (c == '"' && !inSingleQuote) {
+                inDoubleQuote = !inDoubleQuote;
+                continue;
+            }
+
+            if (c == '\'' && !inDoubleQuote) {
+                inSingleQuote = !inSingleQuote;
+                continue;
+            }
+
+            if (Character.isWhitespace(c) && !inDoubleQuote && !inSingleQuote) {
+                if (!current.isEmpty()) {
+                    result.add(current.toString());
+                    current.setLength(0);
+                }
+                continue;
+            }
+
+            current.append(c);
+        }
+
+        if (!current.isEmpty()) {
+            result.add(current.toString());
+        }
+
+        return result;
+    }
+
+    /**
+     * Parse argument names from frontmatter 'arguments' field.
+     * Rejects numeric-only names (which conflict with $0, $1 shorthand).
+     */
+    public static List<String> parseArgumentNames(List<String> argumentNames) {
+        if (argumentNames == null || argumentNames.isEmpty()) {
+            return List.of();
+        }
+        return argumentNames.stream()
+                .filter(name -> name != null && !name.isBlank() && !name.matches("^\\d+$"))
+                .toList();
+    }
+
+    /**
+     * Generate argument hint showing remaining unfilled args.
+     *
+     * @param argNames  argument names from frontmatter
+     * @param typedArgs arguments the user has typed so far
+     * @return hint like "[arg2] [arg3]" or null if all filled
+     */
+    public static String generateProgressiveArgumentHint(List<String> argNames, List<String> typedArgs) {
+        if (argNames == null || argNames.size() <= typedArgs.size()) {
+            return null;
+        }
+        return argNames.subList(typedArgs.size(), argNames.size()).stream()
+                .map(name -> "[" + name + "]")
+                .reduce((a, b) -> a + " " + b)
+                .orElse(null);
+    }
+
+    /**
+     * Substitute argument placeholders in content.
+     * <p>
+     * Order of substitution (matching TS):
+     * <ol>
+     *   <li>Named arguments: $foo, $bar → mapped by position from argumentNames</li>
+     *   <li>Indexed access: $ARGUMENTS[0], $ARGUMENTS[1], …</li>
+     *   <li>Shorthand indexed: $0, $1, …</li>
+     *   <li>Full arguments: $ARGUMENTS → raw args string</li>
+     *   <li>Auto-append: if no placeholder matched and args non-empty, append "ARGUMENTS: {args}"</li>
+     * </ol>
+     *
+     * @param content              the content containing placeholders
+     * @param args                 the raw arguments string (null = no args, return unchanged)
+     * @param appendIfNoPlaceholder if true, appends "ARGUMENTS: {args}" when no placeholder found
+     * @param argumentNames        named arguments from frontmatter
+     */
+    public static String substituteArguments(String content, String args,
+                                             boolean appendIfNoPlaceholder,
+                                             List<String> argumentNames) {
+        if (content == null) return "";
+        // null means no args provided — return content unchanged
+        if (args == null) return content;
+
+        List<String> parsedArgs = parseArguments(args);
+        List<String> validNames = parseArgumentNames(argumentNames);
+        String original = content;
+
+        // 1. Replace named arguments: $foo, $bar (not followed by [ or word chars)
+        for (int i = 0; i < validNames.size(); i++) {
+            String name = validNames.get(i);
+            String value = i < parsedArgs.size() ? parsedArgs.get(i) : "";
+            // Match $name but not $name[…] or $nameXxx
+            content = content.replaceAll("\\$" + Pattern.quote(name) + "(?![\\[\\w])",
+                    Matcher.quoteReplacement(value));
+        }
+
+        // 2. Replace indexed: $ARGUMENTS[0], $ARGUMENTS[1], …
+        content = INDEXED_PATTERN.matcher(content).replaceAll(mr -> {
+            int idx = Integer.parseInt(mr.group(1));
+            return Matcher.quoteReplacement(idx < parsedArgs.size() ? parsedArgs.get(idx) : "");
+        });
+
+        // 3. Replace shorthand: $0, $1, …
+        content = SHORTHAND_PATTERN.matcher(content).replaceAll(mr -> {
+            int idx = Integer.parseInt(mr.group(1));
+            return Matcher.quoteReplacement(idx < parsedArgs.size() ? parsedArgs.get(idx) : "");
+        });
+
+        // 4. Replace $ARGUMENTS with full raw args string
+        content = content.replace("$ARGUMENTS", args);
+
+        // 5. Auto-append if no placeholder found and args non-empty
+        if (content.equals(original) && appendIfNoPlaceholder && !args.isBlank()) {
+            content = content + "\n\nARGUMENTS: " + args;
+        }
+
+        return content;
+    }
+
+    /**
+     * Overload with default appendIfNoPlaceholder=true, no named args.
+     */
+    public static String substituteArguments(String content, String args) {
+        return substituteArguments(content, args, true, List.of());
+    }
+}

src/main/java/com/claudecode/util/PromptShellExecution.java

@@ -0,0 +1,150 @@
+package com.claudecode.util;
+
+import com.claudecode.tool.ToolContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Executes embedded shell commands in skill/command markdown content.
+ * Aligns with claude-code/src/utils/promptShellExecution.ts.
+ * <p>
+ * Supported syntaxes:
+ * <ul>
+ *   <li>Code blocks: ```! command ```</li>
+ *   <li>Inline: !`command`</li>
+ * </ul>
+ * <p>
+ * Commands are executed via the system shell (bash or powershell as specified
+ * in frontmatter). Output replaces the command placeholder in the content.
+ */
+public final class PromptShellExecution {
+
+    private static final Logger log = LoggerFactory.getLogger(PromptShellExecution.class);
+
+    private PromptShellExecution() {}
+
+    /** Pattern for code blocks: ```! command ``` */
+    private static final Pattern BLOCK_PATTERN = Pattern.compile("```!\\s*\\n?([\\s\\S]*?)\\n?```");
+
+    /** Pattern for inline: !`command` (preceded by whitespace or start-of-line) */
+    private static final Pattern INLINE_PATTERN = Pattern.compile("(?<=^|\\s)!`([^`]+)`", Pattern.MULTILINE);
+
+    /** Default command timeout in seconds */
+    private static final int DEFAULT_TIMEOUT = 30;
+
+    /**
+     * Parse and execute embedded shell commands in the given text.
+     * Replaces each command placeholder with its output.
+     *
+     * @param text    the skill/command markdown content
+     * @param shell   "bash" or "powershell" (null defaults to bash)
+     * @param workDir working directory for command execution
+     * @return content with command outputs substituted
+     */
+    public static String executeShellCommandsInPrompt(String text, String shell, Path workDir) {
+        if (text == null || text.isEmpty()) return text;
+
+        // Collect all matches (block + inline)
+        List<CommandMatch> matches = new ArrayList<>();
+
+        Matcher blockMatcher = BLOCK_PATTERN.matcher(text);
+        while (blockMatcher.find()) {
+            String command = blockMatcher.group(1);
+            if (command != null && !command.isBlank()) {
+                matches.add(new CommandMatch(blockMatcher.start(), blockMatcher.end(),
+                        blockMatcher.group(0), command.strip()));
+            }
+        }
+
+        // Only scan for inline pattern if text contains !` (optimization from TS)
+        if (text.contains("!`")) {
+            Matcher inlineMatcher = INLINE_PATTERN.matcher(text);
+            while (inlineMatcher.find()) {
+                String command = inlineMatcher.group(1);
+                if (command != null && !command.isBlank()) {
+                    matches.add(new CommandMatch(inlineMatcher.start(), inlineMatcher.end(),
+                            inlineMatcher.group(0), command.strip()));
+                }
+            }
+        }
+
+        if (matches.isEmpty()) return text;
+
+        // Execute commands and replace (reverse order to preserve offsets)
+        matches.sort((a, b) -> Integer.compare(b.start, a.start));
+
+        String result = text;
+        for (CommandMatch match : matches) {
+            try {
+                String output = executeShellCommand(match.command, shell, workDir);
+                result = result.replace(match.fullMatch, output);
+                log.debug("Shell command executed in skill: {} → {} chars output", 
+                        match.command.substring(0, Math.min(50, match.command.length())), output.length());
+            } catch (Exception e) {
+                log.warn("Shell command failed in skill content: {}: {}", match.command, e.getMessage());
+                result = result.replace(match.fullMatch,
+                        "[Error executing command: " + e.getMessage() + "]");
+            }
+        }
+
+        return result;
+    }
+
+    /**
+     * Execute a single shell command and return its stdout.
+     */
+    private static String executeShellCommand(String command, String shell, Path workDir) throws IOException {
+        List<String> cmd;
+        boolean isWindows = System.getProperty("os.name", "").toLowerCase().contains("win");
+
+        if ("powershell".equalsIgnoreCase(shell)) {
+            if (isWindows) {
+                cmd = List.of("powershell", "-NoProfile", "-Command", command);
+            } else {
+                cmd = List.of("pwsh", "-NoProfile", "-Command", command);
+            }
+        } else {
+            // Default: bash
+            if (isWindows) {
+                // Try bash (Git Bash / WSL), fallback to cmd
+                cmd = List.of("bash", "-c", command);
+            } else {
+                cmd = List.of("bash", "-c", command);
+            }
+        }
+
+        ProcessBuilder pb = new ProcessBuilder(cmd);
+        if (workDir != null) {
+            pb.directory(workDir.toFile());
+        }
+        pb.redirectErrorStream(true);
+
+        try {
+            Process process = pb.start();
+            String output = new String(process.getInputStream().readAllBytes());
+            boolean finished = process.waitFor(DEFAULT_TIMEOUT, TimeUnit.SECONDS);
+            if (!finished) {
+                process.destroyForcibly();
+                throw new IOException("Command timed out after " + DEFAULT_TIMEOUT + "s: " + command);
+            }
+            int exitCode = process.exitValue();
+            if (exitCode != 0) {
+                log.debug("Shell command exited with code {}: {}", exitCode, command);
+            }
+            return output.strip();
+        } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
+            throw new IOException("Command interrupted: " + command, e);
+        }
+    }
+
+    private record CommandMatch(int start, int end, String fullMatch, String command) {}
+}

src/test/java/com/claudecode/util/ArgumentSubstitutionTest.java

@@ -0,0 +1,120 @@
+package com.claudecode.util;
+
+import org.junit.jupiter.api.Test;
+
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class ArgumentSubstitutionTest {
+
+    @Test
+    void parseArguments_simpleWhitespace() {
+        assertEquals(List.of("foo", "bar", "baz"), ArgumentSubstitution.parseArguments("foo bar baz"));
+    }
+
+    @Test
+    void parseArguments_doubleQuotedString() {
+        assertEquals(List.of("foo", "hello world", "baz"),
+                ArgumentSubstitution.parseArguments("foo \"hello world\" baz"));
+    }
+
+    @Test
+    void parseArguments_singleQuotedString() {
+        assertEquals(List.of("foo", "hello world", "baz"),
+                ArgumentSubstitution.parseArguments("foo 'hello world' baz"));
+    }
+
+    @Test
+    void parseArguments_escapedSpaces() {
+        assertEquals(List.of("hello world"), ArgumentSubstitution.parseArguments("hello\\ world"));
+    }
+
+    @Test
+    void parseArguments_emptyAndNull() {
+        assertEquals(List.of(), ArgumentSubstitution.parseArguments(null));
+        assertEquals(List.of(), ArgumentSubstitution.parseArguments(""));
+        assertEquals(List.of(), ArgumentSubstitution.parseArguments("   "));
+    }
+
+    @Test
+    void parseArgumentNames_filtersNumericOnly() {
+        assertEquals(List.of("foo", "bar"),
+                ArgumentSubstitution.parseArgumentNames(List.of("foo", "123", "bar", "0")));
+    }
+
+    @Test
+    void substituteArguments_fullArguments() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "Run $ARGUMENTS now", "test.js", true, List.of());
+        assertEquals("Run test.js now", result);
+    }
+
+    @Test
+    void substituteArguments_indexedAccess() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "File: $ARGUMENTS[0] Line: $ARGUMENTS[1]", "test.js 42", true, List.of());
+        assertEquals("File: test.js Line: 42", result);
+    }
+
+    @Test
+    void substituteArguments_shorthandIndexed() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "File: $0 Line: $1", "test.js 42", true, List.of());
+        assertEquals("File: test.js Line: 42", result);
+    }
+
+    @Test
+    void substituteArguments_namedArguments() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "File: $file Line: $line", "test.js 42", true, List.of("file", "line"));
+        assertEquals("File: test.js Line: 42", result);
+    }
+
+    @Test
+    void substituteArguments_quotedMultiWord() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "Greeting: $0", "\"hello world\"", true, List.of());
+        assertEquals("Greeting: hello world", result);
+    }
+
+    @Test
+    void substituteArguments_autoAppendWhenNoPlaceholder() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "No placeholders here.", "some args", true, List.of());
+        assertEquals("No placeholders here.\n\nARGUMENTS: some args", result);
+    }
+
+    @Test
+    void substituteArguments_noAutoAppendWhenDisabled() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "No placeholders here.", "some args", false, List.of());
+        assertEquals("No placeholders here.", result);
+    }
+
+    @Test
+    void substituteArguments_nullArgsUnchanged() {
+        String content = "Content with $ARGUMENTS placeholder";
+        assertSame(content, ArgumentSubstitution.substituteArguments(content, null, true, List.of()));
+    }
+
+    @Test
+    void substituteArguments_emptyArgsReplaces() {
+        String result = ArgumentSubstitution.substituteArguments(
+                "Run $ARGUMENTS now", "", true, List.of());
+        assertEquals("Run  now", result);
+    }
+
+    @Test
+    void generateProgressiveArgumentHint_basic() {
+        assertEquals("[arg2] [arg3]",
+                ArgumentSubstitution.generateProgressiveArgumentHint(
+                        List.of("arg1", "arg2", "arg3"), List.of("val1")));
+    }
+
+    @Test
+    void generateProgressiveArgumentHint_allFilled() {
+        assertNull(ArgumentSubstitution.generateProgressiveArgumentHint(
+                List.of("arg1"), List.of("val1")));
+    }
+}