chore: bump versions for next release

[Jesus Talavera (jesus-talavera-ibm)]

Description

Bump the package versions to release the changes on main that are not in the latest published versions.

Package	Old	New	Reason
qiskit-mcp-server	0.3.1	0.3.2	#222: cap the Qiskit requirement at qiskit>=1.3.0,<3
qiskit-gym-mcp-server	0.4.1	0.4.2	#222: cap the Qiskit requirement at qiskit>=1.3.0,<3
qiskit-ibm-runtime-mcp-server	0.6.1	0.6.2	#225: the README uses the MCP tool names. The README is the PyPI project description.
qiskit-mcp-servers (meta-package)	0.12.0	0.12.1	Raise the minimum versions of the three packages above

qiskit-docs-mcp-server (0.3.0) and qiskit-ibm-transpiler-mcp-server (0.4.1) have no changes since their last release. This PR does not change them.

For each server that gets a new version, this PR changes the version in pyproject.toml and the two version keys in server.json. In uv.lock, only the four workspace version lines change.

Release order after merge

1. Create the releases qiskit-v0.3.2, gym-v0.4.2 and runtime-v0.6.2.
2. Make sure that the three "Publish to PyPI" jobs pass.
3. Create the release meta-v0.12.1. The meta-package requires the new server versions, so release it last.

Linked Issue(s)

None. This PR releases #222 and #225.

Type of change

• Release preparation: version numbers only. No change to the code.

How Has This Been Tested?

• uv run pytest in qiskit-mcp-server: 102 passed
• uv run pytest in qiskit-gym-mcp-server: 97 passed
• uv run pytest in qiskit-ibm-runtime-mcp-server: 205 passed, 1 skipped
• ruff check src tests and ruff format --check src tests in all five servers (same scope as CI): no errors
• Script check: in each server, the version in pyproject.toml is the same as the two version keys in server.json

Test Configuration:

• Firmware version: N/A
• Hardware: macOS (Darwin 25.6.0)
• Toolchain: uv 0.9.9, Python 3.11.14
• SDK: N/A

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas (N/A: version numbers only)
• I have made corresponding changes to the documentation (N/A)
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works (N/A)
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules (not yet: the meta-package requires 0.3.2, 0.4.2 and 0.6.2 on PyPI. See "Release order after merge".)

[//va (vabarbosa)]

thank you!