diff --git a/docs/how-to/install-bmad.md b/docs/how-to/install-bmad.md
index 4fbca560b..4122ecf46 100644
--- a/docs/how-to/install-bmad.md
+++ b/docs/how-to/install-bmad.md
@@ -212,7 +212,7 @@ npx bmad-method install --list-options bmm
 The legacy core shortcuts (`--user-name`, `--output-folder`, etc.) still work and remain documented for backward compatibility, but `--set core.user_name=...` is equivalent and uses the same code path.
 
 :::note[Quick-update is unaffected]
-`bmad install --action quick-update` preserves the existing `config.toml` answers as-is. `--set` flags passed alongside `--action quick-update` are silently ignored. To change a stored value, run `bmad install --action update` (or just `bmad install`) instead.
+`bmad install --action quick-update` preserves the existing `config.toml` answers as-is. `--set` flags passed alongside `--action quick-update` are ignored — the installer prints a warning so scripted runs surface the mismatch in CI logs. To change a stored value, run `bmad install --action update` (or just `bmad install`) instead.
 :::
 
 :::caution[Rate limit on shared IPs]
diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index 2facf8aed..e3bc263ca 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -3084,6 +3084,72 @@ async function runTests() {
 
     await fs.remove(tmp44).catch(() => {});
     await fs.remove(tmp44b).catch(() => {});
+
+    // Integration: --set actually applies through collectModuleConfig with skipPrompts.
+    // Constructs OfficialModules directly (no UI), runs the bmm collector, asserts
+    // the override value lands in collectedConfig with the result template rendered.
+    const tmp44c = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-fixture-44c-'));
+    try {
+      const om = new OfficialModules({
+        setOverrides: { bmm: { project_knowledge: 'research', user_skill_level: 'expert' } },
+      });
+      om.skipPrompts = true;
+      om._silentConfig = true;
+      om.modulesToCustomize = new Set();
+      om.allAnswers = {};
+      om._existingConfig = {};
+      await om.collectModuleConfig('bmm', tmp44c, true, true);
+
+      assert(
+        om.collectedConfig.bmm?.project_knowledge === '{project-root}/research',
+        'collectModuleConfig pre-fills bmm.project_knowledge from --set and renders {project-root}/{value}',
+      );
+      assert(
+        om.collectedConfig.bmm?.user_skill_level === 'expert',
+        'collectModuleConfig pre-fills bmm.user_skill_level from --set ({value} template)',
+      );
+      // Unrelated bmm keys still get their schema defaults applied.
+      assert(
+        typeof om.collectedConfig.bmm?.planning_artifacts === 'string',
+        'collectModuleConfig still fills non-overridden bmm keys with schema defaults under skipPrompts',
+      );
+    } catch (error) {
+      console.log(`${colors.red}  collectModuleConfig --set integration failed: ${error.message}${colors.reset}`);
+      console.log(error.stack);
+      failed++;
+    }
+    await fs.remove(tmp44c).catch(() => {});
+
+    // Carry-forward: an unknown key persisted by a prior install survives the
+    // next collectModuleConfig even when --set isn't repeated. This is the
+    // "persist across upgrades" contract from #1663 (CodeRabbit major fix).
+    const tmp44d = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-fixture-44d-'));
+    try {
+      const om = new OfficialModules();
+      om.skipPrompts = true;
+      om._silentConfig = true;
+      om.modulesToCustomize = new Set();
+      om.allAnswers = {};
+      // Simulate prior install: future_thing was --set on run #1, persisted to
+      // _bmad/bmm/config.yaml, and is now loaded as _existingConfig.
+      om._existingConfig = { bmm: { future_thing: 'pre-seeded', user_skill_level: 'beginner' } };
+      await om.collectModuleConfig('bmm', tmp44d, true, true);
+
+      assert(om.collectedConfig.bmm?.future_thing === 'pre-seeded', 'collectModuleConfig carries unknown key forward from _existingConfig');
+      assert(
+        om.setOverrideKeys?.bmm?.has('future_thing'),
+        'carried-forward keys are tracked in setOverrideKeys so writeCentralConfig keeps them',
+      );
+      // Declared keys from _existingConfig are NOT carried forward by this
+      // mechanism — they go through normal prompt processing and would be
+      // seeded as defaults via buildQuestion's existingValue lookup.
+      assert(!om.setOverrideKeys?.bmm?.has('user_skill_level'), 'carry-forward leaves declared keys to the normal prompt path');
+    } catch (error) {
+      console.log(`${colors.red}  collectModuleConfig carry-forward failed: ${error.message}${colors.reset}`);
+      console.log(error.stack);
+      failed++;
+    }
+    await fs.remove(tmp44d).catch(() => {});
   } catch (error) {
     console.log(`${colors.red}Test Suite 44 setup failed: ${error.message}${colors.reset}`);
     console.log(error.stack);
diff --git a/tools/installer/commands/install.js b/tools/installer/commands/install.js
index d752b0471..02bc67525 100644
--- a/tools/installer/commands/install.js
+++ b/tools/installer/commands/install.js
@@ -19,8 +19,8 @@ module.exports = {
     ],
     ['--list-tools', 'Print all supported tool/IDE IDs (with target directories) and exit.'],
     [
-      '--set <key=value>',
-      'Set a module config option non-interactively. Format: <module>.<key>=<value> (e.g. bmm.project_knowledge=research). Repeatable. Run --list-options to see available keys.',
+      '--set <module.key=value>',
+      'Set a module config option non-interactively (e.g. --set bmm.project_knowledge=research). Repeatable. Run --list-options to see available keys.',
       (value, prev) => [...(prev || []), value],
       [],
     ],
diff --git a/tools/installer/list-options.js b/tools/installer/list-options.js
index 37742143e..3009423d1 100644
--- a/tools/installer/list-options.js
+++ b/tools/installer/list-options.js
@@ -33,6 +33,14 @@ async function readModuleCode(yamlPath) {
  */
 async function discoverOfficialModuleYamls() {
   const found = [];
+  // Dedupe is case-insensitive because module caches occasionally retain a
+  // legacy UPPERCASE-named directory alongside the canonical lowercase one
+  // (same module, different cache key from an older schema). We pick whichever
+  // entry we see first and skip the alternate-case duplicate. NOTE: `--set`
+  // matching itself is case-sensitive (it keys on `moduleName` from the install
+  // flow's selected list, which is always lowercase short codes), so the
+  // surfaced `code` here is what users should type. Don't change to
+  // case-sensitive dedupe without revisiting that contract.
   const seenCodes = new Set();
 
   const addFound = async (yamlPath, source, fallbackCode) => {
@@ -120,7 +128,7 @@ function formatModuleOptions(code, parsed, source) {
     lines.push(`  ${code}.${key}    (${type}${scope})  default: ${defaultStr}`);
     const promptText = formatPromptText(item);
     if (promptText) lines.push(`    ${promptText}`);
-    if (item['single-select']) {
+    if (Array.isArray(item['single-select'])) {
       const values = item['single-select'].map((v) => (typeof v === 'object' ? v.value : v)).filter((v) => v !== undefined);
       if (values.length > 0) lines.push(`    values: ${values.join(' | ')}`);
     }
diff --git a/tools/installer/modules/official-modules.js b/tools/installer/modules/official-modules.js
index 964e5d248..5a1437337 100644
--- a/tools/installer/modules/official-modules.js
+++ b/tools/installer/modules/official-modules.js
@@ -27,6 +27,57 @@ class OfficialModules {
     this.setOverrides = options.setOverrides || {};
   }
 
+  /**
+   * Apply `--set <module>.<key>=<value>` overrides AFTER normal collection.
+   *
+   * Used for modules whose `collectModuleConfig` was skipped — currently only
+   * `core`, when its config was seeded by `--yes` defaults or by legacy
+   * core-shortcut flags (--user-name/--output-folder/etc.). For all other
+   * modules, override handling is integrated into `collectModuleConfig`.
+   *
+   * Validates known keys against the module's `module.yaml` schema (located
+   * via `getModulePath`); unknown keys are warned but persisted, mirroring
+   * the schema-handling for non-core modules. Core's `result:` templates are
+   * all `{value}` (or `{project-root}/{value}` for `output_folder`, which the
+   * legacy flag handlers also write raw), so writing the raw override value
+   * preserves parity with the `--user-name` / `--output-folder` shortcuts.
+   *
+   * @param {string} moduleName
+   */
+  async applyOverridesAfterSeeding(moduleName) {
+    const overrides = this.setOverrides[moduleName] || {};
+    if (Object.keys(overrides).length === 0) return;
+
+    if (!this.collectedConfig[moduleName]) this.collectedConfig[moduleName] = {};
+    for (const [key, value] of Object.entries(overrides)) {
+      this.collectedConfig[moduleName][key] = value;
+    }
+
+    let schema = null;
+    const schemaPath = path.join(getModulePath(moduleName), 'module.yaml');
+    if (await fs.pathExists(schemaPath)) {
+      try {
+        schema = yaml.parse(await fs.readFile(schemaPath, 'utf8'));
+      } catch {
+        // schema unparseable — skip key-existence validation
+      }
+    }
+    if (!schema || typeof schema !== 'object') return;
+
+    if (!this.setOverrideKeys) this.setOverrideKeys = {};
+    if (!this.setOverrideKeys[moduleName]) this.setOverrideKeys[moduleName] = new Set();
+    for (const key of Object.keys(overrides)) {
+      const decl = schema[key];
+      const isDeclared = decl && typeof decl === 'object' && 'prompt' in decl;
+      if (!isDeclared) {
+        await prompts.log.warn(
+          `--set ${moduleName}.${key} — '${key}' is not a declared config key for module '${moduleName}'; persisted but unused by current install.`,
+        );
+        this.setOverrideKeys[moduleName].add(key);
+      }
+    }
+  }
+
   /**
    * Module configurations collected during install.
    */
@@ -1561,12 +1612,13 @@ class OfficialModules {
     }
     // Drop pre-seeded questions so the user is not re-prompted and so
     // skipPrompts mode doesn't overwrite the override with the default.
-    const remainingQuestions = questions.filter((q) => {
-      const key = q.name.replace(`${moduleName}_`, '');
-      return !seededOverrideKeys.has(key);
-    });
-    questions.length = 0;
-    questions.push(...remainingQuestions);
+    // In-place mutation keeps the rest of this method's `questions` references
+    // pointing at the filtered list without renaming a local through 100+ lines.
+    if (seededOverrideKeys.size > 0) {
+      const remaining = questions.filter((q) => !seededOverrideKeys.has(q.name.replace(`${moduleName}_`, '')));
+      questions.length = 0;
+      questions.push(...remaining);
+    }
 
     if (seededOverrideKeys.size > 0 && !this._silentConfig) {
       const list = [...seededOverrideKeys].map((k) => `${moduleName}.${k}`).join(', ');
@@ -1791,6 +1843,34 @@ class OfficialModules {
       }
     }
 
+    // Carry forward unknown keys persisted by a prior install. Without this,
+    // a value originally set via `--set <module>.future_thing=...` lands in
+    // `_bmad/<module>/config.yaml` on run #1, but the next collectModuleConfig
+    // rebuilds collectedConfig from prompt answers only — the unknown key
+    // would be silently dropped from the regenerated config.toml. Tracking
+    // the carried keys in setOverrideKeys ensures the schema-strict partition
+    // in writeCentralConfig keeps them. (#1663 forward-compat contract)
+    const priorConfig = this._existingConfig?.[moduleName];
+    if (priorConfig && typeof priorConfig === 'object' && !Array.isArray(priorConfig)) {
+      const declaredAndStaticKeys = new Set(declaredPromptKeys);
+      for (const key of configKeys) {
+        const item = moduleConfig[key];
+        if (item && typeof item === 'object' && item.result && !item.prompt) {
+          declaredAndStaticKeys.add(key);
+        }
+      }
+      for (const [key, value] of Object.entries(priorConfig)) {
+        if (declaredAndStaticKeys.has(key)) continue;
+        // Already written by this run (e.g. via unknown --set above): leave alone.
+        if (this.collectedConfig[moduleName] && key in this.collectedConfig[moduleName]) continue;
+        if (!this.collectedConfig[moduleName]) this.collectedConfig[moduleName] = {};
+        if (!this.setOverrideKeys) this.setOverrideKeys = {};
+        if (!this.setOverrideKeys[moduleName]) this.setOverrideKeys[moduleName] = new Set();
+        this.collectedConfig[moduleName][key] = value;
+        this.setOverrideKeys[moduleName].add(key);
+      }
+    }
+
     await this.displayModulePostConfigNotes(moduleName, moduleConfig);
   }
 
diff --git a/tools/installer/set-overrides.js b/tools/installer/set-overrides.js
index b5db532ae..f47ae553a 100644
--- a/tools/installer/set-overrides.js
+++ b/tools/installer/set-overrides.js
@@ -1,8 +1,3 @@
-const path = require('node:path');
-const fs = require('./fs-native');
-const yaml = require('yaml');
-const { getModulePath, getExternalModuleCachePath } = require('./project-root');
-
 /**
  * Parse a single `--set <module>.<key>=<value>` entry.
  * @param {string} entry - raw flag value
@@ -18,6 +13,9 @@ function parseSetEntry(entry) {
     throw new Error(`--set "${entry}": missing '='. Expected <module>.<key>=<value>`);
   }
   const lhs = entry.slice(0, eq);
+  // Note: only the LHS is trimmed. Values may legitimately contain leading
+  // or trailing whitespace (paths with spaces, quoted strings); module / key
+  // names cannot, so it's safe to be strict on the left.
   const value = entry.slice(eq + 1);
   const dot = lhs.indexOf('.');
   if (dot === -1) {
@@ -48,48 +46,4 @@ function parseSetEntries(entries) {
   return overrides;
 }
 
-/**
- * Find a module's source `module.yaml` for officials only.
- * Returns null for community/custom; we don't validate those.
- * @param {string} moduleCode
- * @returns {Promise<string|null>}
- */
-async function findOfficialModuleYaml(moduleCode) {
-  const builtIn = path.join(getModulePath(moduleCode), 'module.yaml');
-  if (await fs.pathExists(builtIn)) return builtIn;
-
-  const externalRoot = getExternalModuleCachePath(moduleCode);
-  if (!(await fs.pathExists(externalRoot))) return null;
-
-  const candidates = [
-    path.join(externalRoot, 'module.yaml'),
-    path.join(externalRoot, 'src', 'module.yaml'),
-    path.join(externalRoot, 'skills', 'module.yaml'),
-  ];
-  for (const candidate of candidates) {
-    if (await fs.pathExists(candidate)) return candidate;
-  }
-  return null;
-}
-
-/**
- * Read declared config keys (those with a `prompt:`) from a module.yaml.
- * Returns a Set of key names, or null if the file can't be read.
- */
-async function readDeclaredKeys(moduleYamlPath) {
-  try {
-    const parsed = yaml.parse(await fs.readFile(moduleYamlPath, 'utf8'));
-    if (!parsed || typeof parsed !== 'object') return null;
-    const keys = new Set();
-    for (const [key, value] of Object.entries(parsed)) {
-      if (value && typeof value === 'object' && 'prompt' in value) {
-        keys.add(key);
-      }
-    }
-    return keys;
-  } catch {
-    return null;
-  }
-}
-
-module.exports = { parseSetEntry, parseSetEntries, findOfficialModuleYaml, readDeclaredKeys };
+module.exports = { parseSetEntry, parseSetEntries };
diff --git a/tools/installer/ui.js b/tools/installer/ui.js
index 22b94ec7e..12867dfd5 100644
--- a/tools/installer/ui.js
+++ b/tools/installer/ui.js
@@ -797,41 +797,13 @@ class UI {
       skipPrompts: options.yes || false,
     });
 
-    // Apply --set overrides for `core` AFTER collectAllConfigurations, since
-    // core is skipped when its config was seeded by `--yes` defaults or by
-    // legacy core-shortcut flags (--user-name/--output-folder/etc.). Without
-    // this step those override values would be silently dropped. Core
-    // result templates are all `{value}` (or `{project-root}/{value}` for
-    // output_folder, which the existing flag handling also writes raw),
-    // so writing the raw value matches the legacy shortcut semantics.
-    const coreOverrides = setOverrides.core || {};
-    if (Object.keys(coreOverrides).length > 0) {
-      if (!configCollector.collectedConfig.core) configCollector.collectedConfig.core = {};
-      for (const [key, value] of Object.entries(coreOverrides)) {
-        configCollector.collectedConfig.core[key] = value;
-      }
-      const yaml = require('yaml');
-      const { getProjectRoot } = require('./project-root');
-      const coreSchemaPath = path.join(getProjectRoot(), 'src', 'core-skills', 'module.yaml');
-      let coreSchema = null;
-      try {
-        coreSchema = yaml.parse(await fs.readFile(coreSchemaPath, 'utf8'));
-      } catch {
-        // schema unavailable — skip key-existence validation
-      }
-      if (coreSchema) {
-        if (!configCollector.setOverrideKeys) configCollector.setOverrideKeys = {};
-        if (!configCollector.setOverrideKeys.core) configCollector.setOverrideKeys.core = new Set();
-        for (const key of Object.keys(coreOverrides)) {
-          if (!(key in coreSchema)) {
-            await prompts.log.warn(
-              `--set core.${key} — '${key}' is not a declared config key for module 'core'; persisted but unused by current install.`,
-            );
-            configCollector.setOverrideKeys.core.add(key);
-          }
-        }
-      }
-    }
+    // Apply --set overrides for `core` AFTER collectAllConfigurations.
+    // Core is skipped inside collectAllConfigurations when its config was
+    // seeded by `--yes` defaults or by legacy core-shortcut flags
+    // (--user-name/--output-folder/etc.), so its overrides need a separate
+    // application path. Non-core modules apply overrides inside their own
+    // collectModuleConfig run.
+    await configCollector.applyOverridesAfterSeeding('core');
 
     // Convert per-module override-key Sets to plain string arrays so the value
     // round-trips cleanly through Config.build / freezing.