Updated TR alignment should

[maxaalexeeva]

• include alignment on bigrams
• be case-sensitive for identifiers
• have thresholds for when to return links, e.g., for gvar -> param setting through identifier (for the same paper), the threshold has to be very high
• have indication of which variables are likely related, e.g., I, I(0), I(t), etc.
• handle equations that contain mainly text, e.g., PPE ~ use ~ of ~ an ~ item ~ on ~ a ~ particular ~ day = \frac{(\# ~ of ~ patients ~ that ~ day) (\# ~ of ~ daily ~ cont acts ~ per ~ patient)}{\# ~ of ~ patient ~ contacts ~ before ~ discarding ~ item}
• have the option to align text to src directly if comments are not available