Fix documentation sync after PR #704 default mode change to namespace

[Copilot]

The documentation was out of sync with the breaking change introduced in PR #704, which changed the default behavior of azmcp server start from exposing all individual tools (~128 tools) to namespace-level tools (~25 tools).

What was fixed

Before this fix:

• Documentation incorrectly described the default mode as exposing "all tools individually"
• Manual install examples were inconsistent and confusing
• Server mode documentation referenced outdated behavior
• No clear migration path for users wanting the old behavior

After this fix:

• All documentation correctly describes namespace mode as the default
• Clear examples showing both default behavior and --mode all for individual tools
• Added prominent notice about the v0.5.0 breaking change with reference link
• Consistent terminology across all documentation files

Files updated

• README.md: Added breaking change notice with reference link, restructured manual install examples, updated custom client examples
• CONTRIBUTING.md: Fixed server modes section to reflect correct default behavior and standardized terminology
• docs/azmcp-commands.md: Removed redundant sections, clarified default behavior, added version context
• TROUBLESHOOTING.md: Updated server mode examples to reflect new defaults

Key improvements

The documentation now clearly explains that:

• azmcp server start uses namespace mode by default (since v0.5.0)
• azmcp server start --mode all restores pre-v0.5.0 behavior with individual tools
• The change helps prevent VS Code from hitting the 128 tool limit
• Users have clear migration paths depending on their needs
• Consistent terminology distinguishes "Namespace Mode" (default) from "Namespace Filtering" (service-specific filtering)

Fixes #781.

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[Copilot]

Pull Request Overview

This PR fixes documentation that became out of sync with the breaking change introduced in PR #704, which changed the default behavior of azmcp server start from exposing all individual tools (~128 tools) to namespace-level tools (~25 tools).

• Updated documentation to correctly reflect namespace mode as the default behavior
• Added prominent breaking change notices and migration guidance for users
• Restructured examples to show both default behavior and --mode all for individual tools

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
docs/azmcp-commands.md	Clarified default mode descriptions, added version context, removed redundant sections
TROUBLESHOOTING.md	Updated server mode examples to reflect new defaults
README.md	Added breaking change notice, restructured manual install examples with clear configuration options
CONTRIBUTING.md	Fixed server modes section terminology and updated example configurations

Comments suppressed due to low confidence (2)

docs/azmcp-commands.md:27

• [nitpick] The heading uses inconsistent capitalization. 'Namespace-level' should use lowercase 'l' for consistency with other headings in the file.

#### Default Mode (Namespace-level Tools)

CONTRIBUTING.md:176

• [nitpick] The terminology is inconsistent with the docs/azmcp-commands.md file which uses 'Namespace-level Tools'. Consider using consistent naming across documentation files.

**Default Mode (Namespace)** - namespace-level tools (default behavior):

[joshfree]

Left some consistency suggestions

[jongio]

Sorry for the inconvenience, but we have moved the Azure MCP Server source code to https://github.com/microsoft/mcp. This change allows us to build any Microsoft MCP server with the same engineering system and allows us to brand any MCP server with either Azure or Microsoft branding. This repo change means that you need to move this PR to that new repo. Please do so and then add a link here to that new PR. We'll close this PR now and we look forward to seeing this over on the new repo.