Restructure docs for clarity and discoverability

[drbergman]

Reorganize the documentation around user intent so the sidebar is scannable and newcomers can find where to look:

• Regroup the sidebar by task: Getting Started, Building & Varying Models, Experiments, Analyzing Results, Examples, Tools, Reference, Contributing, API Reference, Miscellaneous.
• Split the dense getting-started page into Installation, Julia environments (new), Your first project, and Importing a project.
• Add an Examples cookbook hub and rewrite the home page as a "Where do I look?" hub.
• Group the API reference by code family (independent of the Manual); keep the alphabetical Index for name lookup.
• Editorial concision pass over every manual page (no facts, examples, or @refs removed); fix two pre-existing broken cross-references.

Verified: docs build passes cross-reference and nav validation.

[Copilot]

Pull request overview

This PR reorganizes the Documenter.jl documentation to be task-oriented and easier to navigate for new and returning users of PhysiCellModelManager.jl, including new “Installation”, “Julia environments”, and “Examples” hub pages and a grouped API reference sidebar.

Changes:

• Restructures the docs sidebar into intent-based sections and groups the API reference by “code family” (docs/make.jl).
• Splits and rewrites getting-started material into focused pages (Installation, Julia environments, first project, importing projects) and adds an Examples cookbook hub.
• Performs an editorial concision pass across many manual pages while preserving technical content and references.

Reviewed changes

Copilot reviewed 21 out of 22 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
progress.md	Adds a changelog entry describing the docs restructure, rationale, and verification notes.
docs/make.jl	Rebuilds the docs navigation into intent-based groups and hand-maintained API reference groupings.
docs/src/index.md	Rewrites the landing page into a “Where do I look?” hub with task-to-page links.
docs/src/man/xml_path_helpers.md	Renames page title and tightens descriptions/examples for XML path helper functions.
docs/src/man/varying_parameters.md	Clarifies XML-path representation and streamlines how-to guidance for variations.
docs/src/man/sensitivity_analysis.md	Condenses and clarifies method descriptions and setup guidance.
docs/src/man/querying_parameters.md	Improves readability of parameter-querying options and descriptions.
docs/src/man/project_configuration.md	Clarifies inputs.toml location and what initialization parses from it.
docs/src/man/physicell_studio.md	Tightens wording and improves internal cross-reference usage.
docs/src/man/latent_variations.md	Rewrites overview/requirements for latent variations for clarity and correctness.
docs/src/man/julia_environments.md	New page introducing Julia per-project environments and recommended workflow.
docs/src/man/intracellular_inputs.md	Tightens explanation of intracellular inputs workflow and example.
docs/src/man/installation.md	New installation guide (JuliaUp + registry + package install) with next steps.
docs/src/man/importing_projects.md	New focused guide for importing existing PhysiCell projects into PCMM projects.
docs/src/man/getting_started.md	Refactors “Getting started” into “Your first project” happy-path page.
docs/src/man/examples.md	New task-oriented cookbook hub with short recipes and links to deeper pages.
docs/src/man/data_directory.md	Updates data-directory documentation to align with createProject and clearer naming.
docs/src/man/covariations.md	Condenses narrative; retains examples and refines explanations/footnotes.
docs/src/man/calibration.md	Minor clarity edits around distance functions and mseDistance notes.
docs/src/man/best_practices.md	Adds environment best-practice and tightens guidance wording.
docs/src/man/analyzing_output.md	Improves concision/clarity of plotting and data-loading documentation.

Comments suppressed due to low confidence (1)

docs/src/man/covariations.md:60

• This snippet uses Uniform(...) from Distributions.jl without importing Distributions, so it won’t run when copy/pasted.

```julia
apop_xml_path = configPath("default", "apoptosis", "death_rate")
apop_dist = Uniform(0, 0.001)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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