Refresh outdated dependency and reporting documentation

[coisa]

Problem

The documentation around packaged dependencies and reporting is no longer aligned with the current behavior of the project. In particular, docs/links/dependencies.rst is outdated, related command pages still describe older dependency, metrics, and reports behavior, and the README command examples no longer match the current command surface.

Current Behavior

Several documentation surfaces still refer to previous package choices or previous command behavior, for example:

• outdated dependency package names in docs/links/dependencies.rst
• incomplete or stale dependencies command behavior in command and running guides
• reports documentation that does not fully reflect the current metrics integration
• README command examples that do not match the current Composer-facing usage
• API or overview pages that still summarize commands with outdated wording

Expected Behavior

The documentation SHOULD consistently describe the current packaged dependencies, dependency analysis workflow, metrics generation, and reports pipeline across reference, command, running, architecture-oriented pages, and the repository README.

Failure Surface

Affected surfaces may include, but are not limited to:

• README.md
• docs/links/dependencies.rst
• docs/commands/dependencies.rst
• docs/running/specialized-commands.rst
• docs/commands/reports.rst
• docs/running/reports.rst
• docs/api/commands.rst
• any nearby page that still describes superseded command behavior or dependency choices

Proposal

Audit the documentation pages related to dependencies and reports, then update the outdated pages so they describe the current repository behavior and packaged toolchain.

Implementation Strategy

Start from docs/links/dependencies.rst, then follow the affected command and workflow pages until the dependency and reporting narrative is internally consistent again. Include README command examples in the same pass so the top-level usage guidance matches the detailed documentation.

Non-goals

• Redesigning the overall documentation architecture
• Introducing new commands or changing runtime behavior to match old docs
• Rewriting unrelated sections that are already accurate

Acceptance Criteria

Documentation Criteria

• docs/links/dependencies.rst reflects the current direct dependencies and their purpose.
• The dependencies command documentation matches the current preview-by-default and --upgrade behavior.
• Reports and metrics documentation reflects the current reports pipeline, including metrics integration where applicable.
• README command examples and summaries match the current Composer-facing usage.
• Any other documentation page touched by the same drift is updated in the same pass so the affected narrative is consistent.

Verification Criteria

• The updated pages use current command names, options, package names, and generated artifact paths.
• Cross-page descriptions no longer contradict the implemented command behavior.

Architectural / Isolation Criteria

• Keep the change scoped to documentation and documentation-adjacent generated references.
• Preserve the current documentation structure unless a small local edit is required for clarity.
• Avoid bundling unrelated product or workflow changes into the same issue.