diff --git a/src/commands/amend/config.ts b/src/commands/amend/config.ts
index 192e1b93..7cd65aec 100644
--- a/src/commands/amend/config.ts
+++ b/src/commands/amend/config.ts
@@ -55,5 +55,14 @@ export const options = {
 } as Record<string, Options>
 
 export const builder = (yargs: Argv) => {
-  return yargs.options(options).usage(getCommandUsageHeader(command))
+  return yargs
+    .options(options)
+    .check((argv) => {
+      const a = argv as { dryRun?: boolean; apply?: boolean }
+      if (a.dryRun && a.apply) {
+        throw new Error('--dry-run and --apply cannot be combined — --dry-run previews, --apply amends.')
+      }
+      return true
+    })
+    .usage(getCommandUsageHeader(command))
 }
diff --git a/src/commands/amend/configCheck.test.ts b/src/commands/amend/configCheck.test.ts
new file mode 100644
index 00000000..dc86406b
--- /dev/null
+++ b/src/commands/amend/configCheck.test.ts
@@ -0,0 +1,44 @@
+import { Argv } from 'yargs'
+import { builder } from './config'
+
+// The builder's `.check()` callback enforces --dry-run/--apply mutual
+// exclusion (#1889). Exercise it directly against a minimal yargs-chain
+// stub instead of a full `.parseSync()`, since yargs' default failure
+// handler calls `process.exit` on a thrown check error rather than
+// propagating it to the test.
+function extractCheckFn(): (argv: Record<string, unknown>) => boolean {
+  let captured: ((argv: Record<string, unknown>) => boolean) | undefined
+  const fakeYargs = {
+    options: () => fakeYargs,
+    check: (fn: (argv: Record<string, unknown>) => boolean) => {
+      captured = fn
+      return fakeYargs
+    },
+    usage: () => fakeYargs,
+  }
+  builder(fakeYargs as unknown as Argv)
+  if (!captured) throw new Error('builder did not register a .check() callback')
+  return captured
+}
+
+describe('amend config validation (#1889)', () => {
+  const check = extractCheckFn()
+
+  it('rejects --dry-run combined with --apply', () => {
+    expect(() => check({ dryRun: true, apply: true })).toThrow(
+      '--dry-run and --apply cannot be combined — --dry-run previews, --apply amends.'
+    )
+  })
+
+  it('accepts --dry-run alone', () => {
+    expect(check({ dryRun: true })).toBe(true)
+  })
+
+  it('accepts --apply alone', () => {
+    expect(check({ apply: true })).toBe(true)
+  })
+
+  it('accepts neither flag', () => {
+    expect(check({})).toBe(true)
+  })
+})
diff --git a/src/commands/changelog/changelog.test.ts b/src/commands/changelog/changelog.test.ts
index 79124b1a..a1741c1f 100644
--- a/src/commands/changelog/changelog.test.ts
+++ b/src/commands/changelog/changelog.test.ts
@@ -10,6 +10,7 @@ import { getRepo } from '../../lib/simple-git/getRepo'
 import { getCommitLogCurrentBranch } from '../../lib/simple-git/getCommitLogCurrentBranch'
 import { getCommitLogRangeDetails } from '../../lib/simple-git/getCommitLogRangeDetails'
 import { getCurrentBranchName } from '../../lib/simple-git/getCurrentBranchName'
+import { getDiffForBranch } from '../../lib/simple-git/getDiffForBranch'
 import { executeChain } from '../../lib/langchain/utils/executeChain'
 import { loadConfig } from '../../lib/config/utils/loadConfig'
 import { getApiKeyForModel, getModelAndProviderFromConfig } from '../../lib/langchain/utils'
@@ -59,6 +60,7 @@ const mockGetCommitLogCurrentBranch = getCommitLogCurrentBranch as jest.MockedFu
   typeof getCommitLogCurrentBranch
 >
 const mockGetCurrentBranchName = getCurrentBranchName as jest.MockedFunction<typeof getCurrentBranchName>
+const mockGetDiffForBranch = getDiffForBranch as jest.MockedFunction<typeof getDiffForBranch>
 const mockGetCommitLogRangeDetails = getCommitLogRangeDetails as jest.MockedFunction<
   typeof getCommitLogRangeDetails
 >
@@ -449,4 +451,76 @@ describe('changelog command', () => {
       )
     })
   })
+
+  describe('--only-diff (#1889)', () => {
+    it('rejects --only-diff combined with --range instead of silently ignoring --range', async () => {
+      argv.onlyDiff = true
+      mockLoadConfig.mockReturnValue({
+        service: {
+          authentication: { type: 'APIKey', credentials: { apiKey: 'mock-api-key' } },
+          provider: 'openai',
+          model: 'gpt-4o',
+          tokenLimit: 4096,
+          temperature: 0.2,
+          maxConcurrent: 1,
+        },
+        defaultBranch: 'main',
+        mode: 'stdout',
+        range: 'abc123:def456',
+      } as unknown as Config)
+
+      await expect(handler(argv, logger)).rejects.toMatchObject({ name: 'CommandExitError', code: 1 })
+      expect(logger.error).toHaveBeenCalledWith(
+        expect.stringContaining('--only-diff'),
+        expect.anything()
+      )
+    })
+
+    it('rejects --only-diff combined with --tag instead of silently ignoring --tag', async () => {
+      argv.onlyDiff = true
+      argv.tag = 'v1.0.0'
+
+      await expect(handler(argv, logger)).rejects.toMatchObject({ name: 'CommandExitError', code: 1 })
+      expect(logger.error).toHaveBeenCalledWith(
+        expect.stringContaining('--only-diff'),
+        expect.anything()
+      )
+    })
+
+    it('rejects --only-diff combined with --since-last-tag instead of silently ignoring it', async () => {
+      argv.onlyDiff = true
+      mockLoadConfig.mockReturnValue({
+        service: {
+          authentication: { type: 'APIKey', credentials: { apiKey: 'mock-api-key' } },
+          provider: 'openai',
+          model: 'gpt-4o',
+          tokenLimit: 4096,
+          temperature: 0.2,
+          maxConcurrent: 1,
+        },
+        defaultBranch: 'main',
+        mode: 'stdout',
+        sinceLastTag: true,
+      } as unknown as Config)
+
+      await expect(handler(argv, logger)).rejects.toMatchObject({ name: 'CommandExitError', code: 1 })
+      expect(logger.error).toHaveBeenCalledWith(
+        expect.stringContaining('--only-diff'),
+        expect.anything()
+      )
+    })
+
+    it('still allows --only-diff combined with --branch (branch is the diff base)', async () => {
+      argv.onlyDiff = true
+      argv.branch = 'develop'
+      mockGetDiffForBranch.mockResolvedValue({ staged: [], unstaged: [], untracked: [] })
+
+      await handler(argv, logger)
+
+      expect(logger.error).not.toHaveBeenCalled()
+      expect(mockGetDiffForBranch).toHaveBeenCalledWith(
+        expect.objectContaining({ baseBranch: 'develop' })
+      )
+    })
+  })
 })
diff --git a/src/commands/changelog/handler.ts b/src/commands/changelog/handler.ts
index c1692eb2..a991d7ea 100644
--- a/src/commands/changelog/handler.ts
+++ b/src/commands/changelog/handler.ts
@@ -111,6 +111,19 @@ export async function generateChangelogResult(
     commandExit(1)
   }
 
+  if (argv.onlyDiff) {
+    const ignoredByOnlyDiff = [
+      config.range ? '--range' : null,
+      argv.tag ? '--tag' : null,
+      config.sinceLastTag ? '--since-last-tag' : null,
+    ].filter(Boolean)
+
+    if (ignoredByOnlyDiff.length > 0) {
+      logger.error(`--only-diff cannot be combined with ${ignoredByOnlyDiff.join(', ')}.`, { color: 'red' })
+      commandExit(1)
+    }
+  }
+
   if (config.service.authentication.type !== 'None' && !key) {
     handleMissingApiKey(logger, config, { command: 'changelog' })
   }
diff --git a/src/commands/commit/config.ts b/src/commands/commit/config.ts
index 00fbfd9e..57ee0550 100644
--- a/src/commands/commit/config.ts
+++ b/src/commands/commit/config.ts
@@ -164,5 +164,49 @@ export const options = {
 } as Record<string, Options>
 
 export const builder = (yargs: Argv) => {
-  return yargs.options(options).usage(getCommandUsageHeader(command))
+  return yargs
+    .options(options)
+    .check((argv) => {
+      const a = argv as {
+        json?: boolean
+        split?: boolean
+        plan?: boolean
+        apply?: boolean
+        strictSplit?: boolean
+        printMessage?: boolean
+        _: Array<string | number>
+      }
+      const positionalSplit = a._.includes('split')
+      const splitMode = Boolean(a.split || a.plan || positionalSplit)
+
+      // handler.ts:58 already rejects `--json` combined with `--split`,
+      // `--plan`, or `--apply` — emitting a structured `emitJson({ error })`
+      // payload for machine consumers instead of exiting via yargs' plain-text
+      // `.fail()` handler. `.check()` runs during yargs parsing, strictly
+      // before the handler, so any of the rules below that only fire because
+      // one of those three flags is set must defer to that handler-level
+      // check instead of throwing here first. Rules that don't depend on
+      // split/plan/apply (e.g. `--strict-split` with none of them set) aren't
+      // covered by that handler guard, so they still validate here even
+      // under `--json`.
+      const jsonHandledByCommand = Boolean(a.json && (a.split || a.plan || a.apply))
+      if (jsonHandledByCommand) {
+        return true
+      }
+
+      if (a.plan && a.apply) {
+        throw new Error('--plan and --apply cannot be combined — --plan previews, --apply commits.')
+      }
+      if (a.printMessage && (a.split || a.plan || a.apply || a.strictSplit)) {
+        throw new Error('--print-message cannot be combined with --split, --plan, --apply, or --strict-split.')
+      }
+      if (a.apply && !splitMode) {
+        throw new Error('--apply requires --split (it applies a split plan).')
+      }
+      if (a.strictSplit && !splitMode) {
+        throw new Error('--strict-split requires --split or --plan.')
+      }
+      return true
+    })
+    .usage(getCommandUsageHeader(command))
 }
diff --git a/src/commands/commit/configCheck.test.ts b/src/commands/commit/configCheck.test.ts
new file mode 100644
index 00000000..15425845
--- /dev/null
+++ b/src/commands/commit/configCheck.test.ts
@@ -0,0 +1,120 @@
+import { Argv } from 'yargs'
+import { builder } from './config'
+
+// The builder's `.check()` callback enforces the mutually-exclusive split
+// flag rules (#1889). Exercise it directly against a minimal yargs-chain
+// stub instead of a full `.parseSync()`, since yargs' default failure
+// handler calls `process.exit` on a thrown check error rather than
+// propagating it to the test.
+function extractCheckFn(): (argv: Record<string, unknown>) => boolean {
+  let captured: ((argv: Record<string, unknown>) => boolean) | undefined
+  const fakeYargs = {
+    options: () => fakeYargs,
+    check: (fn: (argv: Record<string, unknown>) => boolean) => {
+      captured = fn
+      return fakeYargs
+    },
+    usage: () => fakeYargs,
+  }
+  builder(fakeYargs as unknown as Argv)
+  if (!captured) throw new Error('builder did not register a .check() callback')
+  return captured
+}
+
+describe('commit config validation (#1889)', () => {
+  const check = extractCheckFn()
+
+  it('rejects --plan combined with --apply', () => {
+    expect(() => check({ plan: true, apply: true, _: [] })).toThrow(
+      '--plan and --apply cannot be combined — --plan previews, --apply commits.'
+    )
+  })
+
+  it('rejects --print-message combined with --split', () => {
+    expect(() => check({ printMessage: true, split: true, _: [] })).toThrow(
+      '--print-message cannot be combined with --split, --plan, --apply, or --strict-split.'
+    )
+  })
+
+  it('rejects --print-message combined with --plan', () => {
+    expect(() => check({ printMessage: true, plan: true, _: [] })).toThrow(
+      '--print-message cannot be combined with --split, --plan, --apply, or --strict-split.'
+    )
+  })
+
+  it('rejects --apply without --split', () => {
+    expect(() => check({ apply: true, _: [] })).toThrow(
+      '--apply requires --split (it applies a split plan).'
+    )
+  })
+
+  it('rejects --strict-split without --split or --plan', () => {
+    expect(() => check({ strictSplit: true, _: [] })).toThrow(
+      '--strict-split requires --split or --plan.'
+    )
+  })
+
+  it('accepts --split --apply', () => {
+    expect(check({ split: true, apply: true, _: [] })).toBe(true)
+  })
+
+  it('accepts --plan alone', () => {
+    expect(check({ plan: true, _: [] })).toBe(true)
+  })
+
+  it('accepts the `split` positional with --apply', () => {
+    expect(check({ apply: true, _: ['commit', 'split'] })).toBe(true)
+  })
+
+  it('accepts the `split` positional with --strict-split', () => {
+    expect(check({ strictSplit: true, _: ['commit', 'split'] })).toBe(true)
+  })
+
+  it('accepts --print-message alone', () => {
+    expect(check({ printMessage: true, _: [] })).toBe(true)
+  })
+
+  it('accepts no split-related flags', () => {
+    expect(check({ _: [] })).toBe(true)
+  })
+
+  // handler.ts:58 emits a structured `emitJson({ error })` payload when
+  // `--json` is combined with `--split`/`--plan`/`--apply`, for machine
+  // consumers. These combos must NOT throw here — check() runs before the
+  // handler, so throwing would replace that JSON contract with a plain-text
+  // yargs failure (#2039 review feedback).
+  it('defers to the handler for --json + --plan + --apply instead of throwing', () => {
+    expect(check({ json: true, plan: true, apply: true, _: [] })).toBe(true)
+  })
+
+  it('defers to the handler for --json + --apply without --split', () => {
+    expect(check({ json: true, apply: true, _: [] })).toBe(true)
+  })
+
+  it('defers to the handler for --json + --apply + --strict-split without --split', () => {
+    expect(check({ json: true, apply: true, strictSplit: true, _: [] })).toBe(true)
+  })
+
+  it('defers to the handler for --json + --print-message + --split', () => {
+    expect(check({ json: true, printMessage: true, split: true, _: [] })).toBe(true)
+  })
+
+  // `--strict-split` alone isn't covered by handler.ts's json guard (it only
+  // checks split/plan/apply), so it must still be validated here even under
+  // `--json` — otherwise `coco commit --json --strict-split` would silently
+  // fall into the draft-only path and drop `--strict-split` (the exact bug
+  // #1889 was opened to fix).
+  it('still rejects --json + --strict-split without --split or --plan', () => {
+    expect(() => check({ json: true, strictSplit: true, _: [] })).toThrow(
+      '--strict-split requires --split or --plan.'
+    )
+  })
+
+  it('accepts --json alone', () => {
+    expect(check({ json: true, _: [] })).toBe(true)
+  })
+
+  it('accepts --json + --split (handler enforces the json/split conflict)', () => {
+    expect(check({ json: true, split: true, _: [] })).toBe(true)
+  })
+})
diff --git a/src/commands/doctor/config.ts b/src/commands/doctor/config.ts
index 03abb033..b5eec3bc 100644
--- a/src/commands/doctor/config.ts
+++ b/src/commands/doctor/config.ts
@@ -33,5 +33,15 @@ export const options = {
 } as Record<string, Options>
 
 export const builder = (yargs: Argv) => {
-  return yargs.options(options).usage(getCommandUsageHeader(command))
+  return yargs
+    .options(options)
+    .check((argv) => {
+      const a = argv as { clear?: boolean; cost?: boolean; fix?: boolean }
+      const picked = [a.clear && '--clear', a.cost && '--cost', a.fix && '--fix'].filter(Boolean)
+      if (picked.length > 1) {
+        throw new Error(`Options ${picked.join(', ')} cannot be used together.`)
+      }
+      return true
+    })
+    .usage(getCommandUsageHeader(command))
 }
diff --git a/src/commands/doctor/configCheck.test.ts b/src/commands/doctor/configCheck.test.ts
new file mode 100644
index 00000000..4caae346
--- /dev/null
+++ b/src/commands/doctor/configCheck.test.ts
@@ -0,0 +1,60 @@
+import { Argv } from 'yargs'
+import { builder } from './config'
+
+// The builder's `.check()` callback enforces that --clear/--cost/--fix are
+// mutually exclusive (#1889). Exercise it directly against a minimal
+// yargs-chain stub instead of a full `.parseSync()`, since yargs' default
+// failure handler calls `process.exit` on a thrown check error rather than
+// propagating it to the test.
+function extractCheckFn(): (argv: Record<string, unknown>) => boolean {
+  let captured: ((argv: Record<string, unknown>) => boolean) | undefined
+  const fakeYargs = {
+    options: () => fakeYargs,
+    check: (fn: (argv: Record<string, unknown>) => boolean) => {
+      captured = fn
+      return fakeYargs
+    },
+    usage: () => fakeYargs,
+  }
+  builder(fakeYargs as unknown as Argv)
+  if (!captured) throw new Error('builder did not register a .check() callback')
+  return captured
+}
+
+describe('doctor config validation (#1889)', () => {
+  const check = extractCheckFn()
+
+  it('rejects --clear combined with --cost', () => {
+    expect(() => check({ clear: true, cost: true })).toThrow(
+      'Options --clear, --cost cannot be used together.'
+    )
+  })
+
+  it('rejects --clear combined with --fix', () => {
+    expect(() => check({ clear: true, fix: true })).toThrow(
+      'Options --clear, --fix cannot be used together.'
+    )
+  })
+
+  it('rejects --cost combined with --fix', () => {
+    expect(() => check({ cost: true, fix: true })).toThrow(
+      'Options --cost, --fix cannot be used together.'
+    )
+  })
+
+  it('accepts --clear alone', () => {
+    expect(check({ clear: true })).toBe(true)
+  })
+
+  it('accepts --cost alone', () => {
+    expect(check({ cost: true })).toBe(true)
+  })
+
+  it('accepts --fix alone', () => {
+    expect(check({ fix: true })).toBe(true)
+  })
+
+  it('accepts no flags', () => {
+    expect(check({})).toBe(true)
+  })
+})