feat: add --exclude-dir/--exclude-glob CLI flags, skip examples/docs by default, --ci implies summary, add github output format

Author: tcconnally

src/mcts/cli/main.py

@@ -493,7 +493,7 @@ def scan(
         str | None,
         typer.Option(
             "--terminal-format",
-            help="Terminal layout: table, by_tool, by_analyzer, by_severity, summary",
+            help="Terminal layout: table, by_tool, by_analyzer, by_severity, summary, github",
         ),
     ] = None,
     tool_filter: Annotated[
@@ -553,9 +553,23 @@ def scan(
         bool,
         typer.Option(
             "--ci",
-            help="Apply CI gate preset (fail-on-critical, min-score 70) and print score breakdown on failure",
+            help="Apply CI gate preset (fail-on-critical, min-score 70, summary output) and print score breakdown on failure",
         ),
     ] = False,
+    exclude_glob: Annotated[
+        str | None,
+        typer.Option(
+            "--exclude-glob",
+            help="Comma-separated glob patterns for files/dirs to exclude from scan",
+        ),
+    ] = None,
+    exclude_dir: Annotated[
+        str | None,
+        typer.Option(
+            "--exclude-dir",
+            help="Comma-separated directory names to exclude from scan (e.g. examples,docs)",
+        ),
+    ] = None,
     policy: Annotated[
         Path | None,
         typer.Option("--policy", help="Governance policy YAML (default: .mcts/policy.yaml)"),
@@ -660,6 +674,7 @@ def scan(
 
     from mcts.cli.auto import AutoScanError, resolve_auto_scan
     from mcts.cli.machine_wide import run_machine_wide_cli
+    from mcts.core.config import DEFAULT_EXCLUDE_DIRS
     from mcts.governance import evaluate_policy, load_policy
     from mcts.probe.consent import LiveProbeConsentError, live_consent_granted
     from mcts.probe.session import MCPProbeError
@@ -727,6 +742,8 @@ def scan(
     tool_filters = [p.strip() for p in tool_filter.split(",") if p.strip()] if tool_filter else []
     analyzer_filters = [p.strip() for p in analyzer_filter.split(",") if p.strip()] if analyzer_filter else []
     severity_filters = [p.strip() for p in severity_filter.split(",") if p.strip()] if severity_filter else []
+    exclude_globs = [p.strip() for p in exclude_glob.split(",") if p.strip()] if exclude_glob else []
+    extra_exclude_dirs = [p.strip() for p in exclude_dir.split(",") if p.strip()] if exclude_dir else []
     analyzer_list = [p.strip() for p in analyzers.split(",") if p.strip()] if analyzers else []
     technique_filters: list[str] = []
     if technique:
@@ -742,6 +759,9 @@ def scan(
         fail_on_critical = True
         if min_score is None:
             min_score = 70
+        if terminal_format is None:
+            terminal_format = "summary"
+        hide_safe = True
 
     try:
         resolved_theme = get_theme(theme)
@@ -859,6 +879,8 @@ def scan(
         weights_profile=weights_profile,
         corpus_stats_path=corpus_stats_path,
         assets_path=assets_path,
+        exclude_globs=exclude_globs,
+        exclude_dirs=list(DEFAULT_EXCLUDE_DIRS) + extra_exclude_dirs,
     )
 
     try:

src/mcts/discovery/onboarding.py

@@ -27,6 +27,9 @@
         ".mypy_cache",
         ".pytest_cache",
         ".ruff_cache",
+        "examples",
+        "docs",
+        "scripts",
     }
 )
 

src/mcts/discovery/static.py

@@ -25,6 +25,7 @@
     'Server("mcp")',
 )
 
+<<<<<<< Updated upstream
 DEFAULT_SKIP_PATH_PARTS = frozenset(
     {
         "tests",
@@ -43,6 +44,9 @@
         "build",
     }
 )
+=======
+DEFAULT_SKIP_PATH_PARTS = frozenset({"tests", "test", "examples", "docs", "scripts"})
+>>>>>>> Stashed changes
 
 TYPE_HINT_MAP: dict[str, str] = {
     "str": "string",

src/mcts/ui/alternate_formats.py

@@ -32,6 +32,8 @@ def render_report(
         _render_grouped(findings, console, key=lambda f: f.severity.value)
     elif fmt == "summary":
         _render_summary(report, findings, console)
+    elif fmt == "github":
+        _render_github(report, findings, console)
     else:
         raise ValueError(f"Unknown terminal format: {fmt}")
 
@@ -85,3 +87,47 @@ def _render_summary(report: ScanReport, findings: list[Finding], console: Consol
     console.print(line)
     for f in findings[:10]:
         console.print(f"  [{f.severity.value}] {f.title}")
+
+
+def _render_github(report: ScanReport, findings: list[Finding], console: Console) -> None:
+    """Render a concise GitHub-issue-compatible summary in plain text."""
+    from collections import Counter
+
+    sev_counts = Counter(f.severity.value for f in findings)
+    score = report.score_v2 or report.score
+    risk = getattr(score, "risk_level", None) or "unknown"
+
+    lines = [
+        "## MCTS Security Scan",
+        "",
+        f"**Score:** {report.score.overall}/100 | **Risk:** {risk}",
+        f"**Total findings:** {len(findings)}",
+        "",
+        "### Severity Breakdown",
+        "| Severity | Count |",
+        "|---|---|",
+    ]
+    for sev in ("critical", "high", "medium", "low", "info"):
+        if sev_counts.get(sev, 0):
+            lines.append(f"| {sev.capitalize()} | {sev_counts[sev]} |")
+    lines.append("")
+
+    if findings:
+        lines.append("### Top Findings")
+        lines.append("")
+        for f in findings[:15]:
+            tool = f" ({f.tool})" if f.tool else ""
+            source = (f.location.file if f.location else "") or ""
+            if source and len(source) > 80:
+                source = "..." + source[-77:]
+            src = f" — `{source}`" if source else ""
+            lines.append(f"- **[{f.severity.value.upper()}]** {f.title}{tool}{src}")
+
+    lines.append("")
+    lines.append("---")
+    lines.append(
+        "*Scan by [MCTS](https://github.com/tcconnally/MCTS). "
+        "Run `mcts scan . --terminal-format github` for this output.*"
+    )
+
+    console.print("\n".join(lines))