Remove pulse gate mentions and warn of deprecation (#3723)

Closes #3664.

---------

Co-authored-by: Kaelyn Ferris <[email protected]>

Author: abbycross

docs/guides/pulse.ipynb

@@ -39,9 +39,9 @@
     "\n",
     " Pulse-level control on __all__ IBM Quantum® processors has been removed and this tutorial will __not work correctly__ using these QPUs.\n",
     "\n",
-    " If you were using pulse schedules to execute single and two-qubit rotations, use the new [fractional gates](/docs/guides/fractional-gates) feature. Alternatively, if you would like to simulate pulse schedules for you work, check out the [Qiskit Dynamics](https://qiskit-community.github.io/qiskit-dynamics/) package.\n",
+    " If you were using pulse schedules to execute single- and two-qubit rotations, use the new [fractional gates](/docs/guides/fractional-gates) feature. Alternatively, if you would like to simulate pulse schedules for your work, try the [Qiskit Dynamics](https://qiskit-community.github.io/qiskit-dynamics/) package.\n",
     "\n",
-    "Additionally, the `qiskit.pulse` module has been **removed** as of the Qiskit SDK v2.0.0 (but is still supported under the Qiskit SDK v1.4 until September of 2025). See the [pulse migration guide](../migration-guides/pulse-migration) for more information.\n",
+    "Additionally, the `qiskit.pulse` module has been **removed** as of Qiskit SDK v2.0.0. See the [pulse migration guide](/docs/migration-guides/pulse-migration) for more information.\n",
     "\n",
     "</Admonition>"
    ]

docs/guides/represent-quantum-computers.ipynb

@@ -334,7 +334,8 @@
    "id": "6e9aed06",
    "metadata": {},
    "source": [
-    "The default single-qubit gates on _ibm_sherbrooke_ are `rz`, `x`, and `sx`, and the default two-qubit gate is `ecr` (echoed cross-resonance). CX gates are constructed from `ecr` gates, so on some QPUs `ecr` is specified as the two-qubit basis gate, while on others `cx` is the default. The `ecr` gate is the _entangling_ part of the `cx` gate. To use a gate that is not in the basis gate set, follow instructions in the Qiskit SDK API documentation for custom gates using [pulse gates](/docs/api/qiskit/1.4/qiskit.transpiler.passes.PulseGates#pulsegates). In addition to the control gates, there are also `delay` and `measurement` instructions.\n",
+    "The default single-qubit gates on _ibm_sherbrooke_ are `rz`, `x`, and `sx`, and the default two-qubit gate is `ecr` (echoed cross-resonance). CX gates are constructed from `ecr` gates, so on some QPUs `ecr` is specified as the two-qubit basis gate, while on others `cx` is the default. The `ecr` gate is the _entangling_ part of the `cx` gate. In addition to the control gates, there are also `delay` and `measurement` instructions.\n",
+    "\n",
     "\n",
     "<Admonition type=\"note\">\n",
     "    QPUs have default basis gates, but you can choose whatever gates you want, as long as you provide the instruction or add pulse gates (see [Create transpiler passes.](custom-transpiler-pass)) The default basis gates are those that calibrations have been done for on the QPU, so no further instruction/pulse gates need to be provided. For example, on some QPUs `cx` is the default two-qubit gate and `ecr` on others. See the list of possible [native gates and operations](/docs/guides/qpu-information#native-gates) for more details.\n",

docs/guides/transpiler-stages.ipynb

@@ -404,7 +404,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "4339deb5-4947-493b-8940-e68c91311631",
    "metadata": {},
    "outputs": [
@@ -425,7 +425,7 @@
     "ghz.cx(0, range(1, 5))\n",
     "\n",
     "\n",
-    "# Use fake pulse-enabled backend\n",
+    "# Use fake backend\n",
     "backend = FakeWashingtonV2()\n",
     "\n",
     "# Run with optimization level 3 and 'asap' scheduling pass\n",