I am currently reading this paper and this related paper (can also be found here), which explore the connection between Jordan normal forms and adjacency graphs.
Theorem 6 in the first paper reads
Let $f: \mathbb{N} \rightarrow \mathbb{N}$ be a function. Let $\Gamma_n$ be the directed graph associated with $f$ for the natural number $n$, and let $A_n$ be its adjacency matrix. Suppose $$ P = \{Z_1, \ldots, Z_r, C_1, \ldots, C_s\} $$ is a proper partition of $\Gamma_n$, where $Z_1, \ldots, Z_r$ are the cycles and $C_1, \ldots, C_s$ are the chains. Write the lengths of the cycles and chains as $$ \text{len } Z_j = \ell_j \quad (1 \leq j \leq r) \quad \text{and} \quad \text{len } C_j = m_j \quad (1 \leq j \leq s). $$ Let $\omega_j = \exp(2\pi i/\ell_j)$ be a primitive $\ell_j$th root of unity. The Jordan decomposition of $A_n$ contains the following $1 \times 1$ Jordan blocks for the eigenvalues which are roots of unity: $$ J_1(\omega_j^k) \quad \text{for } 1 \leq j \leq r \text{ and } 1 \leq k \leq \ell_j. $$ The Jordan decomposition contains the following blocks associated with the eigenvalue $0$: $$ J_{m_1}(0), J_{m_2}(0), \ldots, J_{m_s}(0). $$
They have also provided further examples to demonstrate how this works in practice. I am trying to better understand their findings with my own examples. But I did not get consistent results. Here is an example with matrix $A$ given by $$ A= \begin{pmatrix} -x & 0 & 1 \\ 0 & x & -1 \\ -1 & -1 & 0 \end{pmatrix} $$ with $x\in {\mathbb R}$ being a parameter. The graph associated with the matrix is with two 2-cycles and 2 self-loops. Possibible partitions that I can come up with are $\{2\}, \{3\}, \{1\}$, or $\{2,3\},\{1\}$ or $\{1,3\}, \{2\}$. From the first partitioning, the theorem implies that eigenvalues are $x,-x,0$, from the second partitioning, I get $-x$ and $\lambda (\lambda-x)=1$, and from the third partitioning I obtain $x$ and $\lambda (x+\lambda)+1=0$ with $\lambda$ being eigenvalues.
On the other hand, from linear algebra we know that A can be written in Jordan form (by similarity transformation) as $$ J(A)= \begin{pmatrix} 0 & 1 & 0 \\ 0 & 0 & 1 \\ 2x & x^2 & 0 \end{pmatrix} $$ where $\det[A]=2x$ and $\operatorname{tr}[A^2]/2=x^2$.The adjacency graph for $J(A)$ then becomes
with a 3-cycle. The eigenvalues then reads $\lambda \propto e^{2i\pi j/3}\sqrt[3]{2x}$ with $j=0,1,2$. While this solution is correct, what I have obtained from applying the theorem to partitions of $A$ is incorrect. In most of such failing examples, the issue arises from the size of cycles when a self-loop and an n-cycle are present in $A$, whereas in the Jordan form $J(A)$, an $(n+1)$-cycle appears.
The theory merely talks about roots of unity, which I have generalized, but what further changes should I consider in the above theorem so that I can get the correct eigenvalues of A in my example just by looking at its adjacency graph?