diff --git a/.github/workflows/artifacts-summary.lock.yml b/.github/workflows/artifacts-summary.lock.yml
index fc8269cdf9..18666a51af 100644
--- a/.github/workflows/artifacts-summary.lock.yml
+++ b/.github/workflows/artifacts-summary.lock.yml
@@ -1336,7 +1336,7 @@ jobs:
           sudo -E awf --env-all \
             --allow-domains api.enterprise.githubcopilot.com,api.github.com,github.com,raw.githubusercontent.com,registry.npmjs.org \
             --log-level info \
-            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool 'github(list_workflow_run_artifacts)' --allow-tool 'github(list_workflow_runs)' --allow-tool 'github(list_workflows)' --allow-tool safeoutputs --allow-tool 'shell(cat)' --allow-tool 'shell(date)' --allow-tool 'shell(echo)' --allow-tool 'shell(grep)' --allow-tool 'shell(head)' --allow-tool 'shell(ls)' --allow-tool 'shell(pwd)' --allow-tool 'shell(sort)' --allow-tool 'shell(tail)' --allow-tool 'shell(uniq)' --allow-tool 'shell(wc)' --allow-tool 'shell(yq)' --allow-tool write --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
+            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool 'github\(list_workflow_run_artifacts\)' --allow-tool 'github\(list_workflow_runs\)' --allow-tool 'github\(list_workflows\)' --allow-tool safeoutputs --allow-tool 'shell\(cat\)' --allow-tool 'shell\(date\)' --allow-tool 'shell\(echo\)' --allow-tool 'shell\(grep\)' --allow-tool 'shell\(head\)' --allow-tool 'shell\(ls\)' --allow-tool 'shell\(pwd\)' --allow-tool 'shell\(sort\)' --allow-tool 'shell\(tail\)' --allow-tool 'shell\(uniq\)' --allow-tool 'shell\(wc\)' --allow-tool 'shell\(yq\)' --allow-tool write --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
             2>&1 | tee /tmp/gh-aw/agent-stdio.log
 
           # Move preserved Copilot logs to expected location
diff --git a/.github/workflows/mcp-inspector.lock.yml b/.github/workflows/mcp-inspector.lock.yml
index 2816618851..cd7417de67 100644
--- a/.github/workflows/mcp-inspector.lock.yml
+++ b/.github/workflows/mcp-inspector.lock.yml
@@ -1874,7 +1874,7 @@ jobs:
           sudo -E awf --env-all \
             --allow-domains api.enterprise.githubcopilot.com,api.github.com,github.com,raw.githubusercontent.com,registry.npmjs.org \
             --log-level info \
-            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool arxiv --allow-tool 'arxiv(get_paper_details)' --allow-tool 'arxiv(get_paper_pdf)' --allow-tool 'arxiv(search_arxiv)' --allow-tool ast-grep --allow-tool 'ast-grep(*)' --allow-tool brave-search --allow-tool 'brave-search(*)' --allow-tool context7 --allow-tool 'context7(get-library-docs)' --allow-tool 'context7(resolve-library-id)' --allow-tool datadog --allow-tool 'datadog(get_datadog_metric)' --allow-tool 'datadog(search_datadog_dashboards)' --allow-tool 'datadog(search_datadog_metrics)' --allow-tool 'datadog(search_datadog_slos)' --allow-tool deepwiki --allow-tool 'deepwiki(ask_question)' --allow-tool 'deepwiki(read_wiki_contents)' --allow-tool 'deepwiki(read_wiki_structure)' --allow-tool fabric-rti --allow-tool 'fabric-rti(get_eventstream)' --allow-tool 'fabric-rti(get_eventstream_definition)' --allow-tool 'fabric-rti(kusto_get_entities_schema)' --allow-tool 'fabric-rti(kusto_get_function_schema)' --allow-tool 'fabric-rti(kusto_get_shots)' --allow-tool 'fabric-rti(kusto_get_table_schema)' --allow-tool 'fabric-rti(kusto_known_services)' --allow-tool 'fabric-rti(kusto_list_databases)' --allow-tool 'fabric-rti(kusto_list_tables)' --allow-tool 'fabric-rti(kusto_query)' --allow-tool 'fabric-rti(kusto_sample_function_data)' --allow-tool 'fabric-rti(kusto_sample_table_data)' --allow-tool 'fabric-rti(list_eventstreams)' --allow-tool gh-aw --allow-tool github --allow-tool markitdown --allow-tool 'markitdown(*)' --allow-tool memory --allow-tool 'memory(delete_memory)' --allow-tool 'memory(list_memories)' --allow-tool 'memory(retrieve_memory)' --allow-tool 'memory(store_memory)' --allow-tool microsoftdocs --allow-tool 'microsoftdocs(*)' --allow-tool notion --allow-tool 'notion(get_database)' --allow-tool 'notion(get_page)' --allow-tool 'notion(query_database)' --allow-tool 'notion(search_pages)' --allow-tool safeoutputs --allow-tool sentry --allow-tool 'sentry(analyze_issue_with_seer)' --allow-tool 'sentry(find_dsns)' --allow-tool 'sentry(find_organizations)' --allow-tool 'sentry(find_projects)' --allow-tool 'sentry(find_releases)' --allow-tool 'sentry(find_teams)' --allow-tool 'sentry(get_doc)' --allow-tool 'sentry(get_event_attachment)' --allow-tool 'sentry(get_issue_details)' --allow-tool 'sentry(get_trace_details)' --allow-tool 'sentry(search_docs requires SENTRY_OPENAI_API_KEY)' --allow-tool 'sentry(search_events)' --allow-tool 'sentry(search_issues)' --allow-tool 'sentry(whoami)' --allow-tool serena --allow-tool 'serena(*)' --allow-tool 'shell(cat)' --allow-tool 'shell(date)' --allow-tool 'shell(echo)' --allow-tool 'shell(grep)' --allow-tool 'shell(head)' --allow-tool 'shell(ls)' --allow-tool 'shell(pwd)' --allow-tool 'shell(sort)' --allow-tool 'shell(tail)' --allow-tool 'shell(uniq)' --allow-tool 'shell(wc)' --allow-tool 'shell(yq)' --allow-tool tavily --allow-tool 'tavily(*)' --allow-tool write --add-dir /tmp/gh-aw/cache-memory/ --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
+            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool arxiv --allow-tool 'arxiv\(get_paper_details\)' --allow-tool 'arxiv\(get_paper_pdf\)' --allow-tool 'arxiv\(search_arxiv\)' --allow-tool ast-grep --allow-tool 'ast-grep\(*\)' --allow-tool brave-search --allow-tool 'brave-search\(*\)' --allow-tool context7 --allow-tool 'context7\(get-library-docs\)' --allow-tool 'context7\(resolve-library-id\)' --allow-tool datadog --allow-tool 'datadog\(get_datadog_metric\)' --allow-tool 'datadog\(search_datadog_dashboards\)' --allow-tool 'datadog\(search_datadog_metrics\)' --allow-tool 'datadog\(search_datadog_slos\)' --allow-tool deepwiki --allow-tool 'deepwiki\(ask_question\)' --allow-tool 'deepwiki\(read_wiki_contents\)' --allow-tool 'deepwiki\(read_wiki_structure\)' --allow-tool fabric-rti --allow-tool 'fabric-rti\(get_eventstream\)' --allow-tool 'fabric-rti\(get_eventstream_definition\)' --allow-tool 'fabric-rti\(kusto_get_entities_schema\)' --allow-tool 'fabric-rti\(kusto_get_function_schema\)' --allow-tool 'fabric-rti\(kusto_get_shots\)' --allow-tool 'fabric-rti\(kusto_get_table_schema\)' --allow-tool 'fabric-rti\(kusto_known_services\)' --allow-tool 'fabric-rti\(kusto_list_databases\)' --allow-tool 'fabric-rti\(kusto_list_tables\)' --allow-tool 'fabric-rti\(kusto_query\)' --allow-tool 'fabric-rti\(kusto_sample_function_data\)' --allow-tool 'fabric-rti\(kusto_sample_table_data\)' --allow-tool 'fabric-rti\(list_eventstreams\)' --allow-tool gh-aw --allow-tool github --allow-tool markitdown --allow-tool 'markitdown\(*\)' --allow-tool memory --allow-tool 'memory\(delete_memory\)' --allow-tool 'memory\(list_memories\)' --allow-tool 'memory\(retrieve_memory\)' --allow-tool 'memory\(store_memory\)' --allow-tool microsoftdocs --allow-tool 'microsoftdocs\(*\)' --allow-tool notion --allow-tool 'notion\(get_database\)' --allow-tool 'notion\(get_page\)' --allow-tool 'notion\(query_database\)' --allow-tool 'notion\(search_pages\)' --allow-tool safeoutputs --allow-tool sentry --allow-tool 'sentry\(analyze_issue_with_seer\)' --allow-tool 'sentry\(find_dsns\)' --allow-tool 'sentry\(find_organizations\)' --allow-tool 'sentry\(find_projects\)' --allow-tool 'sentry\(find_releases\)' --allow-tool 'sentry\(find_teams\)' --allow-tool 'sentry\(get_doc\)' --allow-tool 'sentry\(get_event_attachment\)' --allow-tool 'sentry\(get_issue_details\)' --allow-tool 'sentry\(get_trace_details\)' --allow-tool 'sentry\(search_docs requires SENTRY_OPENAI_API_KEY\)' --allow-tool 'sentry\(search_events\)' --allow-tool 'sentry\(search_issues\)' --allow-tool 'sentry\(whoami\)' --allow-tool serena --allow-tool 'serena\(*\)' --allow-tool 'shell\(cat\)' --allow-tool 'shell\(date\)' --allow-tool 'shell\(echo\)' --allow-tool 'shell\(grep\)' --allow-tool 'shell\(head\)' --allow-tool 'shell\(ls\)' --allow-tool 'shell\(pwd\)' --allow-tool 'shell\(sort\)' --allow-tool 'shell\(tail\)' --allow-tool 'shell\(uniq\)' --allow-tool 'shell\(wc\)' --allow-tool 'shell\(yq\)' --allow-tool tavily --allow-tool 'tavily\(*\)' --allow-tool write --add-dir /tmp/gh-aw/cache-memory/ --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
             2>&1 | tee /tmp/gh-aw/agent-stdio.log
 
           # Move preserved Copilot logs to expected location
diff --git a/.github/workflows/research.lock.yml b/.github/workflows/research.lock.yml
index 9cb015ed35..332470587e 100644
--- a/.github/workflows/research.lock.yml
+++ b/.github/workflows/research.lock.yml
@@ -1257,7 +1257,7 @@ jobs:
           sudo -E awf --env-all \
             --allow-domains api.enterprise.githubcopilot.com,api.github.com,github.com,raw.githubusercontent.com,registry.npmjs.org \
             --log-level info \
-            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool github --allow-tool safeoutputs --allow-tool tavily --allow-tool 'tavily(*)' --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
+            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool github --allow-tool safeoutputs --allow-tool tavily --allow-tool 'tavily\(*\)' --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
             2>&1 | tee /tmp/gh-aw/agent-stdio.log
 
           # Move preserved Copilot logs to expected location
diff --git a/.github/workflows/smoke-copilot.firewall.lock.yml b/.github/workflows/smoke-copilot.firewall.lock.yml
index 66c9f4aca7..4fea03fdcd 100644
--- a/.github/workflows/smoke-copilot.firewall.lock.yml
+++ b/.github/workflows/smoke-copilot.firewall.lock.yml
@@ -1240,7 +1240,7 @@ jobs:
           sudo -E awf --env-all \
             --allow-domains api.enterprise.githubcopilot.com,api.github.com,github.com,raw.githubusercontent.com,registry.npmjs.org \
             --log-level info \
-            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool github --allow-tool safeoutputs --allow-tool 'shell(cat)' --allow-tool 'shell(date)' --allow-tool 'shell(echo)' --allow-tool 'shell(grep)' --allow-tool 'shell(head)' --allow-tool 'shell(ls)' --allow-tool 'shell(pwd)' --allow-tool 'shell(sort)' --allow-tool 'shell(tail)' --allow-tool 'shell(uniq)' --allow-tool 'shell(wc)' --allow-tool 'shell(yq)' --allow-tool write --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
+            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool github --allow-tool safeoutputs --allow-tool 'shell\(cat\)' --allow-tool 'shell\(date\)' --allow-tool 'shell\(echo\)' --allow-tool 'shell\(grep\)' --allow-tool 'shell\(head\)' --allow-tool 'shell\(ls\)' --allow-tool 'shell\(pwd\)' --allow-tool 'shell\(sort\)' --allow-tool 'shell\(tail\)' --allow-tool 'shell\(uniq\)' --allow-tool 'shell\(wc\)' --allow-tool 'shell\(yq\)' --allow-tool write --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
             2>&1 | tee /tmp/gh-aw/agent-stdio.log
 
           # Move preserved Copilot logs to expected location
diff --git a/.github/workflows/smoke-copilot.lock.yml b/.github/workflows/smoke-copilot.lock.yml
index eef9be1142..7ee24500cd 100644
--- a/.github/workflows/smoke-copilot.lock.yml
+++ b/.github/workflows/smoke-copilot.lock.yml
@@ -1240,7 +1240,7 @@ jobs:
           sudo -E awf --env-all \
             --allow-domains api.enterprise.githubcopilot.com,api.github.com,github.com,raw.githubusercontent.com,registry.npmjs.org \
             --log-level info \
-            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool github --allow-tool safeoutputs --allow-tool 'shell(cat)' --allow-tool 'shell(date)' --allow-tool 'shell(echo)' --allow-tool 'shell(grep)' --allow-tool 'shell(head)' --allow-tool 'shell(ls)' --allow-tool 'shell(pwd)' --allow-tool 'shell(sort)' --allow-tool 'shell(tail)' --allow-tool 'shell(uniq)' --allow-tool 'shell(wc)' --allow-tool 'shell(yq)' --allow-tool write --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
+            "npx -y @github/copilot@0.0.351 --add-dir /tmp/gh-aw/ --log-level all --disable-builtin-mcps --allow-tool github --allow-tool safeoutputs --allow-tool 'shell\(cat\)' --allow-tool 'shell\(date\)' --allow-tool 'shell\(echo\)' --allow-tool 'shell\(grep\)' --allow-tool 'shell\(head\)' --allow-tool 'shell\(ls\)' --allow-tool 'shell\(pwd\)' --allow-tool 'shell\(sort\)' --allow-tool 'shell\(tail\)' --allow-tool 'shell\(uniq\)' --allow-tool 'shell\(wc\)' --allow-tool 'shell\(yq\)' --allow-tool write --allow-all-paths --prompt \"\$(cat /tmp/gh-aw/aw-prompts/prompt.txt)\"" \
             2>&1 | tee /tmp/gh-aw/agent-stdio.log
 
           # Move preserved Copilot logs to expected location
diff --git a/pkg/workflow/shell.go b/pkg/workflow/shell.go
index 53946a2dbf..2cab891a28 100644
--- a/pkg/workflow/shell.go
+++ b/pkg/workflow/shell.go
@@ -37,9 +37,12 @@ func shellEscapeArg(arg string) string {
 // shellEscapeCommandString escapes a complete command string (which may already contain
 // quoted arguments) for passing as a single argument to another command.
 // It wraps the command in double quotes and escapes any double quotes, dollar signs,
-// backticks, and backslashes within the command.
+// backticks, backslashes, and parentheses within the command.
 // This is useful when passing a command to wrapper programs like awf that expect
 // the command as a single quoted argument.
+//
+// Special case: Parentheses immediately following $ (i.e., $(...)) are NOT escaped
+// to preserve command substitution syntax.
 func shellEscapeCommandString(cmd string) string {
 	// Escape backslashes first (must be done before other escapes)
 	escaped := strings.ReplaceAll(cmd, "\\", "\\\\")
@@ -49,7 +52,50 @@ func shellEscapeCommandString(cmd string) string {
 	escaped = strings.ReplaceAll(escaped, "$", "\\$")
 	// Escape backticks (to prevent command substitution)
 	escaped = strings.ReplaceAll(escaped, "`", "\\`")
+	
+	// Escape parentheses (to prevent subshell interpretation inside double quotes)
+	// BUT preserve command substitution syntax: \$(...) should remain as \$(...)
+	// We need to escape ( and ) except when they immediately follow \$ (which was $ before escaping)
+	result := make([]byte, 0, len(escaped)*2)
+	for i := 0; i < len(escaped); i++ {
+		ch := escaped[i]
+		if ch == '(' {
+			// Don't escape opening paren if it follows \$
+			if i >= 2 && escaped[i-2] == '\\' && escaped[i-1] == '$' {
+				result = append(result, ch)
+			} else {
+				result = append(result, '\\', ch)
+			}
+		} else if ch == ')' {
+			// Don't escape closing paren if we're inside a \$(...) construct
+			// We need to track by looking backward for matching \$(
+			inCommandSubst := false
+			depth := 1 // We're currently at a ')', so depth starts at 1
+			for j := i - 1; j >= 0; j-- {
+				if escaped[j] == ')' {
+					depth++
+				} else if escaped[j] == '(' {
+					depth--
+					if depth == 0 {
+						// Found the matching opening paren
+						// Check if it's a command substitution \$(
+						if j >= 2 && escaped[j-2] == '\\' && escaped[j-1] == '$' {
+							inCommandSubst = true
+						}
+						break
+					}
+				}
+			}
+			if inCommandSubst {
+				result = append(result, ch)
+			} else {
+				result = append(result, '\\', ch)
+			}
+		} else {
+			result = append(result, ch)
+		}
+	}
 
 	// Wrap in double quotes
-	return "\"" + escaped + "\""
+	return "\"" + string(result) + "\""
 }
diff --git a/pkg/workflow/shell_test.go b/pkg/workflow/shell_test.go
index b578745f87..56b80a7d3b 100644
--- a/pkg/workflow/shell_test.go
+++ b/pkg/workflow/shell_test.go
@@ -68,6 +68,137 @@ func TestShellEscapeArg(t *testing.T) {
 			input:    "\"\"",
 			expected: "\"\"",
 		},
+		// Additional edge cases
+		{
+			name:     "argument with curly braces",
+			input:    "file{1,2,3}.txt",
+			expected: "'file{1,2,3}.txt'",
+		},
+		{
+			name:     "argument with question mark",
+			input:    "file?.txt",
+			expected: "'file?.txt'",
+		},
+		{
+			name:     "argument with pipe",
+			input:    "cmd1|cmd2",
+			expected: "'cmd1|cmd2'",
+		},
+		{
+			name:     "argument with ampersand",
+			input:    "cmd1&cmd2",
+			expected: "'cmd1&cmd2'",
+		},
+		{
+			name:     "argument with semicolon",
+			input:    "cmd1;cmd2",
+			expected: "'cmd1;cmd2'",
+		},
+		{
+			name:     "argument with less than",
+			input:    "input<file",
+			expected: "'input<file'",
+		},
+		{
+			name:     "argument with greater than",
+			input:    "output>file",
+			expected: "'output>file'",
+		},
+		{
+			name:     "argument with backslash",
+			input:    "path\\to\\file",
+			expected: "'path\\to\\file'",
+		},
+		{
+			name:     "argument with backtick",
+			input:    "cmd`date`",
+			expected: "'cmd`date`'",
+		},
+		{
+			name:     "argument with tab",
+			input:    "hello\tworld",
+			expected: "'hello\tworld'",
+		},
+		{
+			name:     "argument with newline",
+			input:    "hello\nworld",
+			expected: "'hello\nworld'",
+		},
+		{
+			name:     "multiple single quotes",
+			input:    "it's can't won't",
+			expected: "'it'\"'\"'s can'\"'\"'t won'\"'\"'t'",
+		},
+		{
+			name:     "empty string",
+			input:    "",
+			expected: "",
+		},
+		{
+			name:     "single character flag",
+			input:    "-v",
+			expected: "-v",
+		},
+		{
+			name:     "path without special characters",
+			input:    "/usr/bin/env",
+			expected: "/usr/bin/env",
+		},
+		{
+			name:     "path with spaces",
+			input:    "/path/with spaces/file",
+			expected: "'/path/with spaces/file'",
+		},
+		{
+			name:     "command substitution pattern",
+			input:    "$(date)",
+			expected: "'$(date)'",
+		},
+		{
+			name:     "variable expansion pattern",
+			input:    "${VAR}",
+			expected: "'${VAR}'",
+		},
+		{
+			name:     "already quoted with extra chars should be escaped",
+			input:    "\"test\"extra",
+			expected: "'\"test\"extra'",
+		},
+		{
+			name:     "single quote at start only",
+			input:    "'incomplete",
+			expected: "''\"'\"'incomplete'",
+		},
+		{
+			name:     "single quote at end only",
+			input:    "incomplete'",
+			expected: "'incomplete'\"'\"''",
+		},
+		{
+			name:     "double quote at start only",
+			input:    "\"incomplete",
+			expected: "'\"incomplete'",
+		},
+		{
+			name:     "double quote at end only",
+			input:    "incomplete\"",
+			expected: "'incomplete\"'",
+		},
+		{
+			name:     "only single quotes",
+			input:    "''",
+			expected: "''",
+		},
+		{
+			name:     "nested parentheses",
+			input:    "func((arg))",
+			expected: "'func((arg))'",
+		},
+		{
+			name:     "mixed brackets and parentheses",
+			input:    "pattern[a-z](test)",
+			expected: "'pattern[a-z](test)'",
+		},
 	}
 
 	for _, tt := range tests {
@@ -106,6 +237,92 @@ func TestShellJoinArgs(t *testing.T) {
 			input:    []string{"copilot", "--add-dir", "/tmp/gh-aw/", "--prompt", "\"$INSTRUCTION\""},
 			expected: "copilot --add-dir /tmp/gh-aw/ --prompt \"$INSTRUCTION\"",
 		},
+		// Additional edge cases
+		{
+			name:     "empty array",
+			input:    []string{},
+			expected: "",
+		},
+		{
+			name:     "single argument",
+			input:    []string{"command"},
+			expected: "command",
+		},
+		{
+			name:     "single argument with spaces",
+			input:    []string{"hello world"},
+			expected: "'hello world'",
+		},
+		{
+			name:     "multiple arguments with spaces",
+			input:    []string{"echo", "hello world", "foo bar"},
+			expected: "echo 'hello world' 'foo bar'",
+		},
+		{
+			name:     "arguments with various quote types",
+			input:    []string{"cmd", "\"quoted\"", "'single'", "mixed\"quote"},
+			expected: "cmd \"quoted\" 'single' 'mixed\"quote'",
+		},
+		{
+			name:     "arguments with command substitution patterns",
+			input:    []string{"echo", "$(date)", "`whoami`"},
+			expected: "echo '$(date)' '`whoami`'",
+		},
+		{
+			name:     "long command with many arguments",
+			input:    []string{"npx", "@github/copilot", "--allow-tool", "shell(cat)", "--allow-tool", "shell(grep)", "--allow-tool", "shell(sed)", "--log-level", "debug"},
+			expected: "npx @github/copilot --allow-tool 'shell(cat)' --allow-tool 'shell(grep)' --allow-tool 'shell(sed)' --log-level debug",
+		},
+		{
+			name:     "arguments with special shell operators",
+			input:    []string{"cmd", "arg1|arg2", "arg3&arg4", "arg5;arg6"},
+			expected: "cmd 'arg1|arg2' 'arg3&arg4' 'arg5;arg6'",
+		},
+		{
+			name:     "arguments with wildcards",
+			input:    []string{"ls", "*.txt", "file?.doc", "test[0-9].log"},
+			expected: "ls '*.txt' 'file?.doc' 'test[0-9].log'",
+		},
+		{
+			name:     "mixed flags and values",
+			input:    []string{"-v", "--verbose", "-f", "file name.txt", "--output", "result.log"},
+			expected: "-v --verbose -f 'file name.txt' --output result.log",
+		},
+		{
+			name:     "arguments with dollar signs",
+			input:    []string{"echo", "$HOME", "$USER", "$PATH"},
+			expected: "echo '$HOME' '$USER' '$PATH'",
+		},
+		{
+			name:     "pre-quoted arguments mixed with unquoted",
+			input:    []string{"cmd", "\"arg1\"", "arg2", "'arg3'", "arg 4"},
+			expected: "cmd \"arg1\" arg2 'arg3' 'arg 4'",
+		},
+		{
+			name:     "arguments with backslashes",
+			input:    []string{"echo", "\\n", "\\t", "path\\to\\file"},
+			expected: "echo '\\n' '\\t' 'path\\to\\file'",
+		},
+		{
+			name:     "arguments with parentheses and brackets",
+			input:    []string{"tool", "func(arg)", "pattern[a-z]", "test{1,2}"},
+			expected: "tool 'func(arg)' 'pattern[a-z]' 'test{1,2}'",
+		},
+		{
+			name:     "empty string arguments",
+			input:    []string{"cmd", "", "arg"},
+			expected: "cmd  arg",
+		},
+		{
+			name:     "arguments with newlines and tabs",
+			input:    []string{"echo", "line1\nline2", "col1\tcol2"},
+			expected: "echo 'line1\nline2' 'col1\tcol2'",
+		},
+		{
+			name:     "single quotes in multiple arguments",
+			input:    []string{"echo", "it's", "can't", "won't"},
+			expected: "echo 'it'\"'\"'s' 'can'\"'\"'t' 'won'\"'\"'t'",
+		},
 	}
 
 	for _, tt := range tests {
@@ -132,7 +349,7 @@ func TestShellEscapeCommandString(t *testing.T) {
 		{
 			name:     "command with single-quoted arguments",
 			input:    "npx --allow-tool 'shell(cat)' --allow-tool 'shell(ls)'",
-			expected: "\"npx --allow-tool 'shell(cat)' --allow-tool 'shell(ls)'\"",
+			expected: "\"npx --allow-tool 'shell\\(cat\\)' --allow-tool 'shell\\(ls\\)'\"",
 		},
 		{
 			name:     "command with double quotes",
@@ -157,7 +374,144 @@ func TestShellEscapeCommandString(t *testing.T) {
 		{
 			name:     "complex copilot command",
 			input:    "npx -y @github/copilot@0.0.351 --allow-tool 'github(list_workflows)' --prompt \"$(cat /tmp/prompt.txt)\"",
-			expected: "\"npx -y @github/copilot@0.0.351 --allow-tool 'github(list_workflows)' --prompt \\\"\\$(cat /tmp/prompt.txt)\\\"\"",
+			expected: "\"npx -y @github/copilot@0.0.351 --allow-tool 'github\\(list_workflows\\)' --prompt \\\"\\$(cat /tmp/prompt.txt)\\\"\"",
+		},
+		// Command substitution edge cases
+		{
+			name:     "nested command substitution",
+			input:    "echo $(echo $(date))",
+			expected: "\"echo \\$(echo \\$(date))\"",
+		},
+		{
+			name:     "multiple command substitutions",
+			input:    "echo $(date) and $(whoami)",
+			expected: "\"echo \\$(date) and \\$(whoami)\"",
+		},
+		{
+			name:     "command substitution with pipes",
+			input:    "echo $(cat file | grep pattern)",
+			expected: "\"echo \\$(cat file | grep pattern)\"",
+		},
+		{
+			name:     "command substitution with parentheses in arguments",
+			input:    "echo $(grep 'pattern(test)' file)",
+			expected: "\"echo \\$(grep 'pattern\\(test\\)' file)\"",
+		},
+		{
+			name:     "command substitution at the end",
+			input:    "prompt \"$(cat /tmp/file)\"",
+			expected: "\"prompt \\\"\\$(cat /tmp/file)\\\"\"",
+		},
+		// Regular parentheses (not command substitution)
+		{
+			name:     "standalone parentheses should be escaped",
+			input:    "echo (test)",
+			expected: "\"echo \\(test\\)\"",
+		},
+		{
+			name:     "multiple levels of parentheses",
+			input:    "echo ((test))",
+			expected: "\"echo \\(\\(test\\)\\)\"",
+		},
+		{
+			name:     "parentheses in quoted strings",
+			input:    "echo 'test(ing)' and \"more(stuff)\"",
+			expected: "\"echo 'test\\(ing\\)' and \\\"more\\(stuff\\)\\\"\"",
+		},
+		// Mixed scenarios
+		{
+			name:     "command substitution and regular parentheses",
+			input:    "echo $(date) and func(arg) and $(cat file)",
+			expected: "\"echo \\$(date) and func\\(arg\\) and \\$(cat file)\"",
+		},
+		{
+			name:     "parentheses before dollar sign (not command substitution)",
+			input:    "echo (prefix)$VAR",
+			expected: "\"echo \\(prefix\\)\\$VAR\"",
+		},
+		// Backslash edge cases
+		{
+			name:     "existing backslash before parenthesis",
+			input:    "echo \\(already escaped\\)",
+			expected: "\"echo \\\\\\(already escaped\\\\\\)\"",
+		},
+		{
+			name:     "backslash before dollar sign",
+			input:    "echo \\$HOME",
+			expected: "\"echo \\\\\\$HOME\"",
+		},
+		// Dollar sign edge cases
+		{
+			name:     "dollar sign without parentheses (variable)",
+			input:    "echo $HOME",
+			expected: "\"echo \\$HOME\"",
+		},
+		{
+			name:     "dollar sign with braces",
+			input:    "echo ${HOME}",
+			expected: "\"echo \\${HOME}\"",
+		},
+		{
+			name:     "multiple dollar signs",
+			input:    "echo $VAR1 $VAR2 $(cmd)",
+			expected: "\"echo \\$VAR1 \\$VAR2 \\$(cmd)\"",
+		},
+		// Quote edge cases
+		{
+			name:     "mixed quotes",
+			input:    "echo \"test\" 'more' $(cmd)",
+			expected: "\"echo \\\"test\\\" 'more' \\$(cmd)\"",
+		},
+		{
+			name:     "escaped quotes in input",
+			input:    "echo \\\"already escaped\\\"",
+			expected: "\"echo \\\\\\\"already escaped\\\\\\\"\"",
+		},
+		// Real-world copilot scenarios
+		{
+			name:     "copilot with multiple shell tools and command substitution",
+			input:    "npx @github/copilot --allow-tool 'shell(cat)' --allow-tool 'shell(grep)' --allow-tool 'shell(sed)' --prompt \"$(cat /tmp/prompt.txt)\"",
+			expected: "\"npx @github/copilot --allow-tool 'shell\\(cat\\)' --allow-tool 'shell\\(grep\\)' --allow-tool 'shell\\(sed\\)' --prompt \\\"\\$(cat /tmp/prompt.txt)\\\"\"",
+		},
+		{
+			name:     "copilot with environment variable and command substitution",
+			input:    "npx @github/copilot --log-dir $LOG_DIR --prompt \"$(cat $PROMPT_FILE)\"",
+			expected: "\"npx @github/copilot --log-dir \\$LOG_DIR --prompt \\\"\\$(cat \\$PROMPT_FILE)\\\"\"",
+		},
+		// Empty and whitespace
+		{
+			name:     "empty string",
+			input:    "",
+			expected: "\"\"",
+		},
+		{
+			name:     "only whitespace",
+			input:    "   ",
+			expected: "\"   \"",
+		},
+		// Special characters combination
+		{
+			name:     "all special characters",
+			input:    "cmd \"quoted\" 'single' $VAR $(subst) `backtick` \\backslash (paren)",
+			expected: "\"cmd \\\"quoted\\\" 'single' \\$VAR \\$(subst) \\`backtick\\` \\\\backslash \\(paren\\)\"",
+		},
+		// Edge case: $ at end of string
+		{
+			name:     "dollar sign at end",
+			input:    "echo test$",
+			expected: "\"echo test\\$\"",
+		},
+		// Edge case: Opening paren at start
+		{
+			name:     "opening paren at start",
+			input:    "(command)",
+			expected: "\"\\(command\\)\"",
+		},
+		// Edge case: Command substitution with escaped characters inside
+		{
+			name:     "command substitution with special chars inside",
+			input:    "echo $(echo \"test\" | grep 'pattern')",
+			expected: "\"echo \\$(echo \\\"test\\\" | grep 'pattern')\"",
 		},
 	}