diff --git a/.gitignore b/.gitignore
index 815a7622..582d2133 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,3 +28,4 @@ gt
 
 # Runtime state
 state.json
+.runtime/
diff --git a/docs/architecture.md b/docs/architecture.md
index 4f098660..549c7b61 100644
--- a/docs/architecture.md
+++ b/docs/architecture.md
@@ -1027,9 +1027,15 @@ The HQ (town root) is created by `gt install`:
 │   ├── beads.db                   # Mayor mail, coordination, handoffs
 │   └── config.yaml
 │
+├── .runtime/                      # Town runtime state (gitignored)
+│   ├── daemon.json                # Daemon PID, heartbeat
+│   ├── deacon.json                # Deacon cycle state
+│   └── agent-requests.json        # Lifecycle requests
+│
 ├── mayor/                         # Mayor configuration and state
 │   ├── town.json                  # {"type": "town", "name": "..."}
 │   ├── rigs.json                  # Registry of managed rigs
+│   ├── config.json                # Town-level config (theme defaults, etc.)
 │   └── state.json                 # Mayor agent state
 │
 ├── rigs/                          # Standard location for rigs
@@ -1042,6 +1048,7 @@ The HQ (town root) is created by `gt install`:
 **Notes**:
 - Mayor's mail is in town beads (`hq-*` issues), not JSONL files
 - Rigs can be in `rigs/` or at HQ root (both work)
+- `.runtime/` is gitignored - contains ephemeral process state
 - See [docs/hq.md](hq.md) for advanced HQ configurations
 
 ### Rig Level
@@ -1050,9 +1057,18 @@ Created by `gt rig add <name> <git-url>`:
 
 ```
 gastown/                           # Rig = container (NOT a git clone)
-├── config.json                    # Rig configuration (git_url, beads prefix)
+├── config.json                    # Rig identity only (type, name, git_url, beads.prefix)
 ├── .beads/ → mayor/rig/.beads     # Symlink to canonical beads in Mayor
 │
+├── settings/                      # Rig behavioral config (git-tracked)
+│   ├── config.json                # Theme, merge_queue, max_workers
+│   └── namepool.json              # Pool settings (style, max)
+│
+├── .runtime/                      # Rig runtime state (gitignored)
+│   ├── witness.json               # Witness process state
+│   ├── refinery.json              # Refinery process state
+│   └── namepool-state.json        # In-use names, overflow counter
+│
 ├── mayor/                         # Mayor's per-rig presence
 │   ├── rig/                       # CANONICAL clone (beads authority)
 │   │   └── .beads/                # Canonical rig beads (prefix: gt-, etc.)
@@ -1073,6 +1089,11 @@ gastown/                           # Rig = container (NOT a git clone)
     └── Toast/                     # Worktree from Mayor's clone
 ```
 
+**Configuration tiers:**
+- **Identity** (`config.json`): Rig name, git_url, beads prefix - rarely changes
+- **Settings** (`settings/`): Behavioral config - git-tracked, shareable
+- **Runtime** (`.runtime/`): Process state - gitignored, transient
+
 **Beads architecture:**
 - Mayor's clone holds the canonical `.beads/` for the rig
 - Rig root symlinks `.beads/` → `mayor/rig/.beads`
@@ -1499,11 +1520,18 @@ sequenceDiagram
 - Simpler role detection
 - Cleaner directory structure
 
-### 5. Visible Config Directory
+### 5. Three-Tier Configuration Architecture
 
-**Decision**: Use `config/` not `.gastown/` for town configuration.
+**Decision**: Separate identity, settings, and runtime into distinct locations:
+- **Identity** (`config.json`): Rig name, git_url, beads prefix - rarely changes
+- **Settings** (`settings/`): Behavioral config - git-tracked, shareable, visible
+- **Runtime** (`.runtime/`): Process state - gitignored, transient
 
-**Rationale**: AI models often miss hidden directories. Visible is better.
+**Rationale**:
+- AI models often miss hidden directories (so `.gastown/` was bad)
+- Identity config rarely changes; behavioral config may change often
+- Runtime state should never be committed
+- `settings/` is visible to agents, unlike hidden `.gastown/`
 
 ### 6. Rig as Container, Not Clone
 
@@ -1838,9 +1866,9 @@ Work is a continuous stream - you can add new issues, spawn new workers, reprior
 }
 ```
 
-### rig.json (Per-Rig Config)
+### rig.json (Per-Rig Identity)
 
-Each rig has a `config.json` at its root:
+Each rig has a `config.json` at its root containing **identity only** (rarely changes):
 
 ```json
 {
@@ -1855,6 +1883,30 @@ Each rig has a `config.json` at its root:
 }
 ```
 
+Behavioral settings live in `settings/config.json` (git-tracked, shareable):
+
+```json
+{
+  "theme": "desert",
+  "merge_queue": {
+    "enabled": true,
+    "auto_merge": true
+  },
+  "max_workers": 5
+}
+```
+
+Runtime state lives in `.runtime/` (gitignored, transient):
+
+```json
+// .runtime/witness.json
+{
+  "state": "running",
+  "started_at": "2024-01-15T10:30:00Z",
+  "stats": { "polecats_spawned": 42 }
+}
+```
+
 The rig's `.beads/` directory is always at the rig root. Gas Town:
 1. Creates `.beads/` when adding a rig (`gt rig add`)
 2. Runs `bd init --prefix <prefix>` to initialize it
diff --git a/docs/hq.md b/docs/hq.md
index a72be914..d2fa6ab2 100644
--- a/docs/hq.md
+++ b/docs/hq.md
@@ -131,12 +131,16 @@ Sometimes you need to run multiple Gas Town systems from the same parent directo
 If Python Gas Town (PGT) and Go Gas Town (GGT) both use `~/ai/`:
 ```
 ~/ai/
-├── .gastown/           # PGT config
+├── .gastown/           # PGT runtime config (hidden)
+├── .runtime/           # GGT runtime state (gitignored)
 ├── .beads/             # Which system owns this?
 ├── mayor/              # PGT mayor? GGT mayor?
 └── gastown/            # PGT rig? GGT rig?
 ```
 
+Note: GGT uses `.runtime/` for runtime state and `settings/` for behavioral config.
+PGT uses `.gastown/` for both.
+
 ### Solutions
 
 **Option 1: Separate HQs (recommended)**
diff --git a/internal/cmd/doctor.go b/internal/cmd/doctor.go
index aef96869..798936aa 100644
--- a/internal/cmd/doctor.go
+++ b/internal/cmd/doctor.go
@@ -70,6 +70,11 @@ func runDoctor(cmd *cobra.Command, args []string) error {
 	d.Register(doctor.NewWispSizeCheck())
 	d.Register(doctor.NewWispStaleCheck())
 
+	// Config architecture checks
+	d.Register(doctor.NewSettingsCheck())
+	d.Register(doctor.NewRuntimeGitignoreCheck())
+	d.Register(doctor.NewLegacyGastownCheck())
+
 	// Run checks
 	var report *doctor.Report
 	if doctorFix {
diff --git a/internal/doctor/config_check.go b/internal/doctor/config_check.go
new file mode 100644
index 00000000..6e46b931
--- /dev/null
+++ b/internal/doctor/config_check.go
@@ -0,0 +1,302 @@
+package doctor
+
+import (
+	"bufio"
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+
+	"github.com/steveyegge/gastown/internal/constants"
+)
+
+// SettingsCheck verifies each rig has a settings/ directory.
+type SettingsCheck struct {
+	FixableCheck
+	missingSettings []string // Cached during Run for use in Fix
+}
+
+// NewSettingsCheck creates a new settings directory check.
+func NewSettingsCheck() *SettingsCheck {
+	return &SettingsCheck{
+		FixableCheck: FixableCheck{
+			BaseCheck: BaseCheck{
+				CheckName:        "rig-settings",
+				CheckDescription: "Check that rigs have settings/ directory",
+			},
+		},
+	}
+}
+
+// Run checks if all rigs have a settings/ directory.
+func (c *SettingsCheck) Run(ctx *CheckContext) *CheckResult {
+	rigs := c.findRigs(ctx.TownRoot)
+	if len(rigs) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No rigs found",
+		}
+	}
+
+	var missing []string
+	var ok int
+
+	for _, rig := range rigs {
+		settingsPath := constants.RigSettingsPath(rig)
+		if _, err := os.Stat(settingsPath); os.IsNotExist(err) {
+			relPath, _ := filepath.Rel(ctx.TownRoot, rig)
+			missing = append(missing, relPath)
+		} else {
+			ok++
+		}
+	}
+
+	// Cache for Fix
+	c.missingSettings = nil
+	for _, rig := range rigs {
+		settingsPath := constants.RigSettingsPath(rig)
+		if _, err := os.Stat(settingsPath); os.IsNotExist(err) {
+			c.missingSettings = append(c.missingSettings, settingsPath)
+		}
+	}
+
+	if len(missing) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: fmt.Sprintf("All %d rig(s) have settings/ directory", ok),
+		}
+	}
+
+	details := make([]string, len(missing))
+	for i, m := range missing {
+		details[i] = fmt.Sprintf("Missing: %s/settings/", m)
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusWarning,
+		Message: fmt.Sprintf("%d rig(s) missing settings/ directory", len(missing)),
+		Details: details,
+		FixHint: "Run 'gt doctor --fix' to create missing directories",
+	}
+}
+
+// Fix creates missing settings/ directories.
+func (c *SettingsCheck) Fix(ctx *CheckContext) error {
+	for _, path := range c.missingSettings {
+		if err := os.MkdirAll(path, 0755); err != nil {
+			return fmt.Errorf("failed to create %s: %w", path, err)
+		}
+	}
+	return nil
+}
+
+// RuntimeGitignoreCheck verifies .runtime/ is gitignored at town and rig levels.
+type RuntimeGitignoreCheck struct {
+	BaseCheck
+}
+
+// NewRuntimeGitignoreCheck creates a new runtime gitignore check.
+func NewRuntimeGitignoreCheck() *RuntimeGitignoreCheck {
+	return &RuntimeGitignoreCheck{
+		BaseCheck: BaseCheck{
+			CheckName:        "runtime-gitignore",
+			CheckDescription: "Check that .runtime/ directories are gitignored",
+		},
+	}
+}
+
+// Run checks if .runtime/ is properly gitignored.
+func (c *RuntimeGitignoreCheck) Run(ctx *CheckContext) *CheckResult {
+	var issues []string
+
+	// Check town-level .gitignore
+	townGitignore := filepath.Join(ctx.TownRoot, ".gitignore")
+	if !c.containsPattern(townGitignore, ".runtime") {
+		issues = append(issues, "Town .gitignore missing .runtime/ pattern")
+	}
+
+	// Check each rig's .gitignore (in their git clones)
+	rigs := c.findRigs(ctx.TownRoot)
+	for _, rig := range rigs {
+		// Check crew members
+		crewPath := filepath.Join(rig, "crew")
+		if crewEntries, err := os.ReadDir(crewPath); err == nil {
+			for _, crew := range crewEntries {
+				if crew.IsDir() && !strings.HasPrefix(crew.Name(), ".") {
+					crewGitignore := filepath.Join(crewPath, crew.Name(), ".gitignore")
+					if !c.containsPattern(crewGitignore, ".runtime") {
+						relPath, _ := filepath.Rel(ctx.TownRoot, filepath.Join(crewPath, crew.Name()))
+						issues = append(issues, fmt.Sprintf("%s .gitignore missing .runtime/ pattern", relPath))
+					}
+				}
+			}
+		}
+	}
+
+	if len(issues) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: ".runtime/ properly gitignored",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusWarning,
+		Message: fmt.Sprintf("%d location(s) missing .runtime gitignore", len(issues)),
+		Details: issues,
+		FixHint: "Add '.runtime/' to .gitignore files",
+	}
+}
+
+// containsPattern checks if a gitignore file contains a pattern.
+func (c *RuntimeGitignoreCheck) containsPattern(gitignorePath, pattern string) bool {
+	file, err := os.Open(gitignorePath)
+	if err != nil {
+		return false // File doesn't exist
+	}
+	defer file.Close()
+
+	scanner := bufio.NewScanner(file)
+	for scanner.Scan() {
+		line := strings.TrimSpace(scanner.Text())
+		// Check for pattern match (with or without trailing slash, with or without glob prefix)
+		// Accept: .runtime, .runtime/, /.runtime, /.runtime/, **/.runtime, **/.runtime/
+		if line == pattern || line == pattern+"/" ||
+			line == "/"+pattern || line == "/"+pattern+"/" ||
+			line == "**/"+pattern || line == "**/"+pattern+"/" {
+			return true
+		}
+	}
+	return false
+}
+
+// findRigs returns rig directories within the town.
+func (c *RuntimeGitignoreCheck) findRigs(townRoot string) []string {
+	return findAllRigs(townRoot)
+}
+
+// LegacyGastownCheck warns if old .gastown/ directories still exist.
+type LegacyGastownCheck struct {
+	FixableCheck
+	legacyDirs []string // Cached during Run for use in Fix
+}
+
+// NewLegacyGastownCheck creates a new legacy gastown check.
+func NewLegacyGastownCheck() *LegacyGastownCheck {
+	return &LegacyGastownCheck{
+		FixableCheck: FixableCheck{
+			BaseCheck: BaseCheck{
+				CheckName:        "legacy-gastown",
+				CheckDescription: "Check for old .gastown/ directories that should be migrated",
+			},
+		},
+	}
+}
+
+// Run checks for legacy .gastown/ directories.
+func (c *LegacyGastownCheck) Run(ctx *CheckContext) *CheckResult {
+	var found []string
+
+	// Check town-level .gastown/
+	townGastown := filepath.Join(ctx.TownRoot, ".gastown")
+	if info, err := os.Stat(townGastown); err == nil && info.IsDir() {
+		found = append(found, ".gastown/ (town root)")
+	}
+
+	// Check each rig for .gastown/
+	rigs := c.findRigs(ctx.TownRoot)
+	for _, rig := range rigs {
+		rigGastown := filepath.Join(rig, ".gastown")
+		if info, err := os.Stat(rigGastown); err == nil && info.IsDir() {
+			relPath, _ := filepath.Rel(ctx.TownRoot, rig)
+			found = append(found, fmt.Sprintf("%s/.gastown/", relPath))
+		}
+	}
+
+	// Cache for Fix
+	c.legacyDirs = nil
+	if info, err := os.Stat(townGastown); err == nil && info.IsDir() {
+		c.legacyDirs = append(c.legacyDirs, townGastown)
+	}
+	for _, rig := range rigs {
+		rigGastown := filepath.Join(rig, ".gastown")
+		if info, err := os.Stat(rigGastown); err == nil && info.IsDir() {
+			c.legacyDirs = append(c.legacyDirs, rigGastown)
+		}
+	}
+
+	if len(found) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No legacy .gastown/ directories found",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusWarning,
+		Message: fmt.Sprintf("%d legacy .gastown/ directory(ies) found", len(found)),
+		Details: found,
+		FixHint: "Run 'gt doctor --fix' to remove after verifying migration is complete",
+	}
+}
+
+// Fix removes legacy .gastown/ directories.
+func (c *LegacyGastownCheck) Fix(ctx *CheckContext) error {
+	for _, dir := range c.legacyDirs {
+		if err := os.RemoveAll(dir); err != nil {
+			return fmt.Errorf("failed to remove %s: %w", dir, err)
+		}
+	}
+	return nil
+}
+
+// findRigs returns rig directories within the town.
+func (c *LegacyGastownCheck) findRigs(townRoot string) []string {
+	return findAllRigs(townRoot)
+}
+
+// findRigs returns rig directories within the town.
+func (c *SettingsCheck) findRigs(townRoot string) []string {
+	return findAllRigs(townRoot)
+}
+
+// findAllRigs is a shared helper that returns all rig directories within a town.
+func findAllRigs(townRoot string) []string {
+	var rigs []string
+
+	entries, err := os.ReadDir(townRoot)
+	if err != nil {
+		return rigs
+	}
+
+	for _, entry := range entries {
+		if !entry.IsDir() {
+			continue
+		}
+		// Skip non-rig directories
+		name := entry.Name()
+		if name == "mayor" || name == ".beads" || strings.HasPrefix(name, ".") {
+			continue
+		}
+
+		rigPath := filepath.Join(townRoot, name)
+
+		// Check if this looks like a rig (has crew/, polecats/, witness/, or refinery/)
+		markers := []string{"crew", "polecats", "witness", "refinery"}
+		for _, marker := range markers {
+			if _, err := os.Stat(filepath.Join(rigPath, marker)); err == nil {
+				rigs = append(rigs, rigPath)
+				break
+			}
+		}
+	}
+
+	return rigs
+}