refactor: pass envOverrides via tmux export instead of disk write

CLAUDE_CODE_EFFORT_LEVEL (and any CLAUDE_CODE_* / OPENCODE_* key) now flows:
  UI dropdown → POST /api/sessions { envOverrides }
             → new Session({ envOverrides })
             → this._envOverrides
             → tmux-manager.buildEnvExports appends `export KEY=<shellescape(VALUE)>`

Previously the API wrote envOverrides to <case>/.claude/settings.local.json, which
created stale state (UI dropdown disagreeing with disk) and polluted user project
directories. Now envOverrides are ephemeral spawn-time state, preserved across
respawnPane cycles via this._envOverrides and across server restart via
SessionState.envOverrides in state.json.

Also removes the now-unused updateCaseEnvVars import from session-routes.ts.

src/web/public/ralph-wizard.js

@@ -1032,6 +1032,10 @@ Object.assign(CodemanApp.prototype, {
     const enabledItems = config.generatedPlan?.filter(i => i.enabled);
 
     try {
+      const envOverrides = this.buildEnvOverrides(
+        this.getCaseSettings(config.caseName),
+        this.loadAppSettingsFromStorage()
+      );
       const res = await fetch('/api/ralph-loop/start', {
         method: 'POST',
         headers: { 'Content-Type': 'application/json' },
@@ -1042,6 +1046,7 @@ Object.assign(CodemanApp.prototype, {
           maxIterations: config.maxIterations || null,
           enableRespawn: config.enableRespawn,
           planItems: enabledItems?.length ? enabledItems : undefined,
+          ...(Object.keys(envOverrides).length > 0 ? { envOverrides } : {}),
         }),
       });
       const data = await res.json();

src/web/public/session-ui.js

@@ -12,6 +12,22 @@
  */
 
 Object.assign(CodemanApp.prototype, {
+  /**
+   * Build envOverrides payload from case + global settings.
+   * Single source of truth for the server-side tmux setenv values.
+   * Keys omitted when value is default/falsy — backend treats unset as "no override".
+   */
+  buildEnvOverrides(caseSettings, globalSettings) {
+    const env = {};
+    if (caseSettings?.agentTeams || globalSettings?.agentTeamsEnabled) {
+      env.CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS = '1';
+    }
+    if (globalSettings?.thinkingEffort) {
+      env.CLAUDE_CODE_EFFORT_LEVEL = globalSettings.thinkingEffort;
+    }
+    return env;
+  },
+
   // ═══════════════════════════════════════════════════════════════
   // Quick Start
   // ═══════════════════════════════════════════════════════════════
@@ -319,10 +335,7 @@ Object.assign(CodemanApp.prototype, {
       // Build env overrides from global + case settings (case overrides global)
       const caseSettings = this.getCaseSettings(caseName);
       const globalSettings = this.loadAppSettingsFromStorage();
-      const envOverrides = {};
-      if (caseSettings.agentTeams || globalSettings.agentTeamsEnabled) {
-        envOverrides.CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS = '1';
-      }
+      const envOverrides = this.buildEnvOverrides(caseSettings, globalSettings);
       const hasEnvOverrides = Object.keys(envOverrides).length > 0;
       const useOpus1m = caseSettings.opusContext1m || globalSettings.opusContext1mEnabled;
       const modelOverride = useOpus1m ? 'opus[1m]' : '';
@@ -526,6 +539,7 @@ Object.assign(CodemanApp.prototype, {
       }
 
       // Quick-start with opencode mode (auto-allow tools by default)
+      const envOverrides = this.buildEnvOverrides(this.getCaseSettings(caseName), this.loadAppSettingsFromStorage());
       const res = await fetch('/api/quick-start', {
         method: 'POST',
         headers: { 'Content-Type': 'application/json' },
@@ -533,6 +547,7 @@ Object.assign(CodemanApp.prototype, {
           caseName,
           mode: 'opencode',
           openCodeConfig: { autoAllowTools: true },
+          ...(Object.keys(envOverrides).length > 0 ? { envOverrides } : {}),
         })
       });
       const data = await res.json();

src/web/public/terminal-ui.js

@@ -953,11 +953,21 @@ Object.assign(CodemanApp.prototype, {
       }
       const name = `w${startNumber}-${dirName}`;
 
-      // Create session with resumeSessionId
+      // Create session with resumeSessionId — include envOverrides so resumed
+      // conversations inherit current UI settings (effort, agent teams, etc.).
+      // Match by path (not basename) so linked/renamed cases still resolve correctly.
+      const matchingCase = (this.cases || []).find((c) => c.path === workingDir);
+      const caseName = matchingCase?.name || workingDir.split('/').pop() || '';
+      const envOverrides = this.buildEnvOverrides(this.getCaseSettings(caseName), this.loadAppSettingsFromStorage());
       const createRes = await fetch('/api/sessions', {
         method: 'POST',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ workingDir, name, resumeSessionId: sessionId }),
+        body: JSON.stringify({
+          workingDir,
+          name,
+          resumeSessionId: sessionId,
+          ...(Object.keys(envOverrides).length > 0 ? { envOverrides } : {}),
+        }),
       });
       const createData = await createRes.json();
       if (!createData.success) throw new Error(createData.error);

src/web/routes/ralph-routes.ts

@@ -14,7 +14,7 @@ import { RespawnController } from '../../respawn-controller.js';
 import { RalphConfigSchema, FixPlanImportSchema, RalphPromptWriteSchema, RalphLoopStartSchema } from '../schemas.js';
 import { SseEvent } from '../sse-events.js';
 import { autoConfigureRalph, CASES_DIR, SETTINGS_PATH, findSessionOrFail, parseBody } from '../route-helpers.js';
-import { writeHooksConfig } from '../../hooks-config.js';
+import { writeHooksConfig, stripCaseEnvKeys } from '../../hooks-config.js';
 import { generateClaudeMd } from '../../templates/claude-md.js';
 import { getLifecycleLog } from '../../session-lifecycle-log.js';
 import type { SessionPort, EventPort, RespawnPort, ConfigPort, InfraPort } from '../ports/index.js';
@@ -268,10 +268,8 @@ export function registerRalphRoutes(
       );
     }
 
-    const { caseName, taskDescription, completionPhrase, maxIterations, enableRespawn, planItems } = parseBody(
-      RalphLoopStartSchema,
-      req.body
-    );
+    const { caseName, taskDescription, completionPhrase, maxIterations, enableRespawn, planItems, envOverrides } =
+      parseBody(RalphLoopStartSchema, req.body);
 
     const casePath = join(CASES_DIR, caseName);
 
@@ -298,6 +296,11 @@ export function registerRalphRoutes(
       }
     }
 
+    // Strip stale disk entries for keys this request is actively setting.
+    if (envOverrides && Object.keys(envOverrides).length > 0) {
+      await stripCaseEnvKeys(casePath, Object.keys(envOverrides));
+    }
+
     // Create session
     const niceConfig = await ctx.getGlobalNiceConfig();
     const rlModelConfig = await ctx.getModelConfig();
@@ -311,6 +314,7 @@ export function registerRalphRoutes(
       model: rlModelConfig?.defaultModel || undefined,
       claudeMode: rlClaudeModeConfig.claudeMode,
       allowedTools: rlClaudeModeConfig.allowedTools,
+      envOverrides,
     });
 
     // Configure Ralph tracker

src/web/routes/session-routes.ts

@@ -44,7 +44,7 @@ import {
   validatePathWithinBase,
 } from '../route-helpers.js';
 import { AUTH_COOKIE_NAME } from '../middleware/auth.js';
-import { writeHooksConfig, updateCaseEnvVars, updateCaseModel } from '../../hooks-config.js';
+import { writeHooksConfig, updateCaseModel, stripCaseEnvKeys } from '../../hooks-config.js';
 import { generateClaudeMd } from '../../templates/claude-md.js';
 import { imageWatcher } from '../../image-watcher.js';
 import { getLifecycleLog } from '../../session-lifecycle-log.js';
@@ -166,9 +166,21 @@ export function registerSessionRoutes(
       }
     }
 
-    // Write env overrides to .claude/settings.local.json if provided
-    if (body.envOverrides && Object.keys(body.envOverrides).length > 0) {
-      await updateCaseEnvVars(workingDir, body.envOverrides);
+    // envOverrides flow through Session → tmux setenv (ephemeral, per-session).
+    //
+    // For keys the caller is actively setting, strip any stale disk entry a prior
+    // Codeman version may have written. Scope limited to:
+    //   - Claude mode (OpenCode doesn't read .claude/settings.local.json)
+    //   - workingDir inside CASES_DIR (Codeman's managed territory — we never mutate
+    //     .claude/settings.local.json in arbitrary user repos that POST /api/sessions
+    //     can target, because those may have hand-authored values).
+    const canStripDisk =
+      body.mode !== 'opencode' &&
+      body.envOverrides &&
+      Object.keys(body.envOverrides).length > 0 &&
+      workingDir.startsWith(CASES_DIR + '/');
+    if (canStripDisk) {
+      await stripCaseEnvKeys(workingDir, Object.keys(body.envOverrides!));
     }
 
     // Write model override to .claude/settings.local.json if provided
@@ -239,6 +251,7 @@ export function registerSessionRoutes(
       allowedTools: claudeModeConfig.allowedTools,
       openCodeConfig: mode === 'opencode' ? body.openCodeConfig : undefined,
       resumeSessionId: validatedResumeId,
+      envOverrides: body.envOverrides,
     });
 
     ctx.addSession(session);
@@ -854,7 +867,11 @@ export function registerSessionRoutes(
       );
     }
 
-    const { prompt, workingDir } = parseBody(QuickRunSchema, req.body, 'Invalid request body');
+    const {
+      prompt,
+      workingDir,
+      envOverrides: runEnvOverrides,
+    } = parseBody(QuickRunSchema, req.body, 'Invalid request body');
 
     if (!prompt.trim()) {
       return createErrorResponse(ApiErrorCode.INVALID_INPUT, 'prompt is required');
@@ -873,7 +890,7 @@ export function registerSessionRoutes(
       }
     }
 
-    const session = new Session({ workingDir: dir });
+    const session = new Session({ workingDir: dir, envOverrides: runEnvOverrides });
     ctx.addSession(session);
     ctx.store.incrementSessionsCreated();
     ctx.persistSessionState(session);
@@ -910,7 +927,12 @@ export function registerSessionRoutes(
       );
     }
 
-    const { caseName = 'testcase', mode = 'claude', openCodeConfig } = parseBody(QuickStartSchema, req.body);
+    const {
+      caseName = 'testcase',
+      mode = 'claude',
+      openCodeConfig,
+      envOverrides,
+    } = parseBody(QuickStartSchema, req.body);
 
     // Check OpenCode availability if requested
     if (mode === 'opencode') {
@@ -962,6 +984,12 @@ export function registerSessionRoutes(
       }
     }
 
+    // Strip stale disk entries for keys this request is actively setting (Claude only —
+    // see POST /api/sessions for full rationale).
+    if (mode !== 'opencode' && envOverrides && Object.keys(envOverrides).length > 0) {
+      await stripCaseEnvKeys(casePath, Object.keys(envOverrides));
+    }
+
     // Create a new session with the case as working directory
     // Apply global Nice priority config and model config from settings
     const niceConfig = await ctx.getGlobalNiceConfig();
@@ -983,6 +1011,7 @@ export function registerSessionRoutes(
       claudeMode: qsClaudeModeConfig.claudeMode,
       allowedTools: qsClaudeModeConfig.allowedTools,
       openCodeConfig: mode === 'opencode' ? openCodeConfig : undefined,
+      envOverrides,
     });
 
     // Auto-detect completion phrase from CLAUDE.md BEFORE broadcasting

src/web/schemas.ts

@@ -178,6 +178,7 @@ export const QuickStartSchema = z.object({
     .optional(),
   mode: z.enum(['claude', 'shell', 'opencode']).optional(),
   openCodeConfig: OpenCodeConfigSchema,
+  envOverrides: safeEnvOverridesSchema,
 });
 
 // ========== Hook Events ==========
@@ -416,6 +417,7 @@ export const FlickerFilterSchema = z.object({
 export const QuickRunSchema = z.object({
   prompt: z.string().min(1).max(100000),
   workingDir: safePathSchema.optional(),
+  envOverrides: safeEnvOverridesSchema,
 });
 
 /** POST /api/scheduled */
@@ -538,6 +540,7 @@ export const RalphLoopStartSchema = z.object({
   completionPhrase: z.string().max(100).default('COMPLETE'),
   maxIterations: z.number().int().min(0).max(1000).nullable().default(10),
   enableRespawn: z.boolean().default(false),
+  envOverrides: safeEnvOverridesSchema,
   planItems: z
     .array(
       z.object({

src/web/server.ts

@@ -40,7 +40,7 @@ import { execSync } from 'node:child_process';
 import { homedir } from 'node:os';
 import { EventEmitter } from 'node:events';
 import { Session, type BackgroundTask } from '../session.js';
-import type { ClaudeMode } from '../types.js';
+import type { ClaudeMode, SessionState } from '../types.js';
 import { RespawnController, RespawnConfig } from '../respawn-controller.js';
 import type { TerminalMultiplexer } from '../mux-interface.js';
 import { createMultiplexer } from '../mux-factory.js';
@@ -731,7 +731,11 @@ export class WebServer extends EventEmitter {
 
   /** Persists full session state including respawn config to state.json */
   private _persistSessionStateNow(session: Session): void {
-    const state = session.toState();
+    // See session-manager.updateSessionState: __envOverrides is an internal disk-only
+    // field kept off SessionState to avoid leaking via API broadcasts.
+    const base = session.toState();
+    const envOverrides = session.getEnvOverridesForPersist();
+    const state = (envOverrides ? { ...base, __envOverrides: envOverrides } : base) as SessionState;
     const controller = this.respawnControllers.get(session.id);
     if (controller) {
       const config = controller.getConfig();
@@ -1631,6 +1635,9 @@ export class WebServer extends EventEmitter {
 
             // Create a session object for this mux session
             const recoveryClaudeMode = await this.getClaudeModeConfig();
+            // Recover envOverrides from the internal __envOverrides field written by
+            // session-manager (see updateSessionState). Cast to read the non-public field.
+            const savedEnvOverrides = (savedState as { __envOverrides?: Record<string, string> })?.__envOverrides;
             const session = new Session({
               id: muxSession.sessionId, // Preserve the original session ID
               workingDir: muxSession.workingDir,
@@ -1641,6 +1648,7 @@ export class WebServer extends EventEmitter {
               muxSession: muxSession, // Pass the existing session so startInteractive() can attach to it
               claudeMode: recoveryClaudeMode.claudeMode,
               allowedTools: recoveryClaudeMode.allowedTools,
+              envOverrides: savedEnvOverrides,
             });
 
             // Update session name if it was a "Restored:" placeholder or doesn't match saved name