fix(cli): disambiguate reused flag names

src/effect/cli_invocation.ts

@@ -94,7 +94,9 @@ function scanCliArguments(arguments_: readonly string[]) {
     const argument = arguments_[index] ?? '';
     const equalsIndex = argument.indexOf('=');
     const flagName = equalsIndex > 0 ? argument.slice(0, equalsIndex) : argument;
-    const valueKind = valueFlagKinds.get(flagName) ?? cliRuntimeValueFlagKinds.get(flagName);
+    const valueKind = booleanFlagNames.has(flagName)
+      ? undefined
+      : (valueFlagKinds.get(flagName) ?? cliRuntimeValueFlagKinds.get(flagName));
     if (valueKind !== undefined) {
       const value = equalsIndex > 0 ? argument.slice(equalsIndex + 1) : arguments_[index + 1];
       if (flagName === '--home') {
@@ -155,7 +157,11 @@ export function normalizeCliArguments(args: readonly string[]): readonly string[
     const current = args[index] ?? '';
     const equalsIndex = current.indexOf('=');
     const inlineName = equalsIndex > 0 ? current.slice(0, equalsIndex) : current;
-    const kind = valueFlagKinds.get(inlineName);
+    // A spelling can be boolean in one command and valued in another (for
+    // example, `init-manifest --replace` versus `remember --replace <uri>`).
+    // Effect's selected command can disambiguate those flags. Rewriting them
+    // here from the global registry would consume a following flag as a value.
+    const kind = booleanFlagNames.has(inlineName) ? undefined : valueFlagKinds.get(inlineName);
     if (!kind) {
       normalized.push(current);
       continue;

test/integration/cli.effect.test.ts

@@ -83,6 +83,81 @@ describe('Effect CLI', () => {
     }
   });
 
+  it('disambiguates reused boolean and value flag names by selected command', async () => {
+    const root = await mkdtemp(join(tmpdir(), 'threadnote-effect-cli-reused-flags-'));
+    const home = join(root, 'home');
+    const firstRepo = join(root, 'first-repo');
+    const secondRepo = join(root, 'second-repo');
+    try {
+      await Promise.all([mkdir(firstRepo), mkdir(secondRepo)]);
+      await Promise.all([
+        execFilePromise('git', ['-C', firstRepo, 'init', '-q']),
+        execFilePromise('git', ['-C', secondRepo, 'init', '-q']),
+      ]);
+
+      const replaceBeforeRepos = await runCli([
+        'init-manifest',
+        '--home',
+        home,
+        '--dry-run',
+        '--replace',
+        '--repo',
+        firstRepo,
+        '--repo',
+        secondRepo,
+      ]);
+      const replaceAfterRepo = await runCli([
+        'init-manifest',
+        '--home',
+        home,
+        '--dry-run',
+        '--repo',
+        firstRepo,
+        '--replace',
+      ]);
+      const updateStatus = await runCli(['update', '--status', '--json'], {
+        THREADNOTE_HOME: home,
+        THREADNOTE_INSTALL_ROOT: join(root, 'install'),
+      });
+      const replacementUri = 'threadnote://user/test/memories/durable/projects/threadnote/old.md';
+      const rememberReplace = await runCli([
+        'remember',
+        '--home',
+        home,
+        '--dry-run',
+        '--text',
+        'replacement',
+        '--project',
+        'threadnote',
+        '--topic',
+        'reused-replace',
+        '--replace',
+        replacementUri,
+      ]);
+      const projectionStatus = await runCli([
+        'projection',
+        'add',
+        '--home',
+        home,
+        '--id',
+        'reused-status',
+        '--vault',
+        root,
+        '--status',
+        'active',
+      ]);
+
+      expect(replaceBeforeRepos.stdout).toContain('name: first-repo');
+      expect(replaceBeforeRepos.stdout).toContain('name: second-repo');
+      expect(replaceAfterRepo.stdout).toContain('name: first-repo');
+      expect(JSON.parse(updateStatus.stdout)).toMatchObject({version: 1});
+      expect(rememberReplace.stdout).toContain(`supersedes: ${replacementUri}`);
+      expect(projectionStatus.stdout).toContain('statuses: active');
+    } finally {
+      await rm(root, {force: true, recursive: true});
+    }
+  });
+
   it('exposes local AI model installation and switching commands', async () => {
     const install = await runCli(['local-ai', 'install', '--help']);
     const switching = await runCli(['local-ai', 'model', 'switch', '--help']);

test/unit/cli-invocation.property.test.ts

@@ -0,0 +1,18 @@
+import fc from 'fast-check';
+import {describe, expect, it} from 'vitest';
+import {normalizeCliArguments} from '../../src/effect/cli.js';
+
+describe('CLI argument normalization properties', () => {
+  it('leaves globally ambiguous option spellings for the selected command parser', () => {
+    fc.assert(
+      fc.property(
+        fc.constantFrom('--replace', '--status'),
+        fc.string({minLength: 1, maxLength: 40}).map(value => `--${value}`),
+        (ambiguousFlag, followingFlag) => {
+          expect(normalizeCliArguments([ambiguousFlag, followingFlag])).toEqual([ambiguousFlag, followingFlag]);
+        },
+      ),
+      {numRuns: 100},
+    );
+  });
+});

test/unit/cli-production-log.test.ts

@@ -53,6 +53,12 @@ describe('CLI production log policy', () => {
       operation: 'migrate-lifecycle',
       writeProductionLog: false,
     });
+    expect(
+      inspectCliInvocation(['init-manifest', '--replace', '--dry-run', '--repo', '/tmp/repository']),
+    ).toMatchObject({
+      operation: 'init-manifest',
+      writeProductionLog: false,
+    });
     for (const command of ['publish', 'publish-artifact', 'publish-bundle']) {
       expect(inspectCliInvocation(['share', command, '--preview'])).toMatchObject({
         operation: 'share',