fix: resolve agent/crew skills paths against project_root, not cwd

[MedviJenka]

Summary

Fixes #6585.

When loading a crew from JSONC (load_crew, load_crew_from_definition,
load_agent_from_definition), every relative path field (tools with the
custom: prefix, output_pydantic/response_format Python refs, etc.) is
resolved against project_root. The agent/crew skills field was the one
exception: it was passed through unresolved in
crewai/project/json_loader.py, and ultimately reached
crewai/skills/loader.py::discover_skills(Path(skill)), which resolves the
path against Path.cwd() at call time instead of project_root.

This meant the same crew definition would succeed or fail purely based on
the process's current working directory at import/call time — e.g. it
works when running a script directly from its own directory, but fails
with FileNotFoundError: Skill search path does not exist or is not a directory: skills when the same code runs as part of a server process
launched from a different cwd (uvicorn, docker, IDE run configs, etc.).

• Adds _resolve_skill_path_strings() in crewai/project/json_loader.py,
  called for the skills field in both _resolve_agent_python_refs (agent
  definitions) and _resolve_crew_python_refs (crew-level skills).
• Filesystem path strings (e.g. "./skills") are rewritten to absolute
  paths resolved against project_root, reusing the existing
  _resolve_project_path helper (same containment rules already applied to
  input_files).
• Registry references (@org/name), inline SKILL.md string content, and
  values already resolved to non-string objects (e.g. via a {"python": ...} reference, or a pre-loaded Skill instance) are left unchanged.
• Only affects JSON/JSONC loading; direct Python Agent(skills=...) /
  Crew(skills=...) usage is unaffected.

Test plan

• Added TestResolveSkillPathStrings unit tests covering: relative
  path resolution against project_root (not cwd), registry refs
  passed through, inline SKILL.md content passed through, pre-loaded
  Skill objects passed through, and non-list values passed through.
• Added test_skills_resolve_relative_to_project_root_not_cwd to
  TestLoadAgentFromDefinition, reproducing the issue's repro case
  end-to-end: agent loaded via load_agent_from_definition with
  skills: ["./skills"] from a cwd other than project_root correctly
  discovers the skill.
• uv run pytest lib/crewai/tests/project/test_json_loader.py — 61
  passed.
• uv run ruff check on changed files — clean.

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 723b6477-44fb-4719-9708-d2a8f6b4c23c

📥 Commits

Reviewing files that changed from the base of the PR and between 69c0308 and b6465dc.

📒 Files selected for processing (2)

• lib/crewai/src/crewai/project/json_loader.py
• lib/crewai/tests/project/test_json_loader.py

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📝 Walkthrough

Walkthrough

The JSON loader now resolves ordinary agent and crew skills paths relative to project_root, while preserving registry references, inline definitions, and preloaded skill objects. Tests cover path resolution when the process working directory differs.

Changes

Skill Path Resolution

Layer / File(s)	Summary
Skill normalization and special references lib/crewai/src/crewai/project/json_loader.py, lib/crewai/tests/project/test_json_loader.py	Skill strings are resolved against project_root; registry references, inline YAML definitions, preloaded objects, and non-list inputs remain unchanged.
Agent and crew loader wiring lib/crewai/src/crewai/project/json_loader.py, lib/crewai/tests/project/test_json_loader.py	Agent and crew Python-reference resolution applies skill normalization, with integration coverage for paths resolved independently of the current working directory.

Suggested reviewers: vinibrsl

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly states the main fix: resolving agent and crew skills paths against project_root instead of cwd.
Description check	✅ Passed	The description is clearly related to the change and accurately explains the skills path resolution fix and tests.
Linked Issues check	✅ Passed	The changes address #6585 by resolving JSONC-loaded skills paths against project_root and preserving the documented exceptions.
Out of Scope Changes check	✅ Passed	The PR stays focused on skills path resolution and matching tests, with no obvious unrelated code changes.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing Touches

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• Create PR with unit tests

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